Multiple sequence alignment - TraesCS1D01G252600

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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 TraesCS1D01G252600 chr1D 100.000 3767 0 0 1 3767 344677242 344673476 0.000000e+00 6957.0
1 TraesCS1D01G252600 chr1D 89.914 1864 167 12 916 2773 344284032 344285880 0.000000e+00 2381.0
2 TraesCS1D01G252600 chr1D 87.255 408 43 8 3345 3747 488701083 488700680 1.230000e-124 457.0
3 TraesCS1D01G252600 chr1A 96.054 2281 63 11 918 3195 444421849 444419593 0.000000e+00 3688.0
4 TraesCS1D01G252600 chr1A 89.861 1874 169 12 916 2783 443869972 443871830 0.000000e+00 2388.0
5 TraesCS1D01G252600 chr1A 93.842 682 41 1 1 681 444422993 444422312 0.000000e+00 1026.0
6 TraesCS1D01G252600 chr1A 89.897 584 45 9 3195 3767 444419559 444418979 0.000000e+00 739.0
7 TraesCS1D01G252600 chr1A 87.449 247 11 7 673 916 444422121 444421892 2.230000e-67 267.0
8 TraesCS1D01G252600 chr1A 100.000 29 0 0 564 592 444423939 444423911 2.000000e-03 54.7
9 TraesCS1D01G252600 chr1B 95.829 1870 75 3 918 2785 465964535 465966403 0.000000e+00 3018.0
10 TraesCS1D01G252600 chr1B 87.966 1878 184 25 917 2783 466288875 466287029 0.000000e+00 2178.0
11 TraesCS1D01G252600 chr1B 88.693 681 37 11 1 681 465963436 465964076 0.000000e+00 795.0
12 TraesCS1D01G252600 chr1B 86.992 246 9 8 673 916 465964269 465964493 4.830000e-64 255.0
13 TraesCS1D01G252600 chr1B 90.323 155 14 1 3192 3345 465967911 465968065 6.380000e-48 202.0
14 TraesCS1D01G252600 chr7B 82.480 1718 284 6 1062 2775 572507609 572505905 0.000000e+00 1489.0
15 TraesCS1D01G252600 chr7B 82.122 1706 293 10 1052 2748 34168284 34169986 0.000000e+00 1450.0
16 TraesCS1D01G252600 chr7D 82.360 1712 291 9 1046 2748 84422149 84420440 0.000000e+00 1478.0
17 TraesCS1D01G252600 chr7D 81.818 1705 300 7 1053 2749 193935048 193936750 0.000000e+00 1423.0
18 TraesCS1D01G252600 chr5A 82.106 1738 289 19 1022 2748 538349067 538350793 0.000000e+00 1467.0
19 TraesCS1D01G252600 chrUn 82.209 1720 282 20 1046 2747 82637376 82635663 0.000000e+00 1459.0
20 TraesCS1D01G252600 chr7A 82.209 1720 282 17 1046 2747 85724260 85725973 0.000000e+00 1459.0
21 TraesCS1D01G252600 chr7A 81.210 1091 200 4 1686 2772 612532263 612531174 0.000000e+00 874.0
22 TraesCS1D01G252600 chr5D 81.797 1736 289 22 1022 2748 424596932 424598649 0.000000e+00 1430.0
23 TraesCS1D01G252600 chr2D 87.059 425 48 6 3344 3762 73595257 73594834 1.220000e-129 473.0
24 TraesCS1D01G252600 chr2D 85.990 414 50 7 3345 3754 621031824 621032233 1.610000e-118 436.0
25 TraesCS1D01G252600 chr6D 86.732 407 47 6 3345 3747 145831017 145830614 2.670000e-121 446.0
26 TraesCS1D01G252600 chr6D 86.667 405 44 9 3345 3746 431196555 431196158 1.240000e-119 440.0
27 TraesCS1D01G252600 chr6D 85.383 431 49 11 3340 3762 259286063 259285639 5.780000e-118 435.0
28 TraesCS1D01G252600 chr6D 79.487 156 20 4 302 445 445835533 445835688 2.390000e-17 100.0
29 TraesCS1D01G252600 chr4B 85.647 425 46 11 3346 3762 17389339 17388922 2.080000e-117 433.0
30 TraesCS1D01G252600 chr4B 85.507 414 53 6 3345 3754 42908254 42908664 3.480000e-115 425.0
31 TraesCS1D01G252600 chr4B 80.357 112 12 7 571 677 473863328 473863222 4.030000e-10 76.8
32 TraesCS1D01G252600 chr2B 85.783 415 50 8 3345 3754 64336446 64336856 7.470000e-117 431.0
33 TraesCS1D01G252600 chr4A 95.833 48 2 0 564 611 32650895 32650942 1.120000e-10 78.7


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 TraesCS1D01G252600 chr1D 344673476 344677242 3766 True 6957.00 6957 100.00000 1 3767 1 chr1D.!!$R1 3766
1 TraesCS1D01G252600 chr1D 344284032 344285880 1848 False 2381.00 2381 89.91400 916 2773 1 chr1D.!!$F1 1857
2 TraesCS1D01G252600 chr1A 443869972 443871830 1858 False 2388.00 2388 89.86100 916 2783 1 chr1A.!!$F1 1867
3 TraesCS1D01G252600 chr1A 444418979 444423939 4960 True 1154.94 3688 93.44840 1 3767 5 chr1A.!!$R1 3766
4 TraesCS1D01G252600 chr1B 466287029 466288875 1846 True 2178.00 2178 87.96600 917 2783 1 chr1B.!!$R1 1866
5 TraesCS1D01G252600 chr1B 465963436 465968065 4629 False 1067.50 3018 90.45925 1 3345 4 chr1B.!!$F1 3344
6 TraesCS1D01G252600 chr7B 572505905 572507609 1704 True 1489.00 1489 82.48000 1062 2775 1 chr7B.!!$R1 1713
7 TraesCS1D01G252600 chr7B 34168284 34169986 1702 False 1450.00 1450 82.12200 1052 2748 1 chr7B.!!$F1 1696
8 TraesCS1D01G252600 chr7D 84420440 84422149 1709 True 1478.00 1478 82.36000 1046 2748 1 chr7D.!!$R1 1702
9 TraesCS1D01G252600 chr7D 193935048 193936750 1702 False 1423.00 1423 81.81800 1053 2749 1 chr7D.!!$F1 1696
10 TraesCS1D01G252600 chr5A 538349067 538350793 1726 False 1467.00 1467 82.10600 1022 2748 1 chr5A.!!$F1 1726
11 TraesCS1D01G252600 chrUn 82635663 82637376 1713 True 1459.00 1459 82.20900 1046 2747 1 chrUn.!!$R1 1701
12 TraesCS1D01G252600 chr7A 85724260 85725973 1713 False 1459.00 1459 82.20900 1046 2747 1 chr7A.!!$F1 1701
13 TraesCS1D01G252600 chr7A 612531174 612532263 1089 True 874.00 874 81.21000 1686 2772 1 chr7A.!!$R1 1086
14 TraesCS1D01G252600 chr5D 424596932 424598649 1717 False 1430.00 1430 81.79700 1022 2748 1 chr5D.!!$F1 1726

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
262 1209 1.227943 GGACTGTCAAGCCAGCACA 60.228 57.895 10.38 0.0 35.83 4.57 F
278 1225 1.747709 CACATTCTCTGGAGGCCAAG 58.252 55.000 5.01 0.0 30.80 3.61 F
2050 3273 2.032634 GGCTTCACGAACGATGGCA 61.033 57.895 0.14 0.0 36.15 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 3106 0.241213 GGAGCGGAAAAGGAACAAGC 59.759 55.000 0.00 0.00 0.0 4.01 R
2751 3995 7.028131 ACCATCATTCCTAATAATCCTCCTCT 58.972 38.462 0.00 0.00 0.0 3.69 R
3611 5994 0.456312 GGTCCTCTCTACAACGCGTG 60.456 60.000 14.98 10.05 0.0 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
28 975 2.489938 ATCAAGCGTATGGGTGTTGT 57.510 45.000 0.00 0.00 0.00 3.32
29 976 2.264005 TCAAGCGTATGGGTGTTGTT 57.736 45.000 0.00 0.00 0.00 2.83
32 979 2.487762 CAAGCGTATGGGTGTTGTTGAT 59.512 45.455 0.00 0.00 0.00 2.57
70 1017 4.638421 AGAGGAAGTGACTAGACAAGATCG 59.362 45.833 0.00 0.00 0.00 3.69
81 1028 4.554363 AAGATCGCCGAGGACGCG 62.554 66.667 3.53 3.53 39.12 6.01
178 1125 1.670674 GCACCAAGACGACGGAATACA 60.671 52.381 0.00 0.00 0.00 2.29
209 1156 3.621715 GGAAAGCCCAACAACGTATCTAG 59.378 47.826 0.00 0.00 34.14 2.43
210 1157 3.975168 AAGCCCAACAACGTATCTAGT 57.025 42.857 0.00 0.00 0.00 2.57
262 1209 1.227943 GGACTGTCAAGCCAGCACA 60.228 57.895 10.38 0.00 35.83 4.57
278 1225 1.747709 CACATTCTCTGGAGGCCAAG 58.252 55.000 5.01 0.00 30.80 3.61
365 1313 7.487829 GTCGAGAAATATCATCTGATTAGCTCC 59.512 40.741 0.00 0.00 36.05 4.70
475 1423 8.575589 ACACACAAAGTTTGAGCATATTTGATA 58.424 29.630 22.23 0.00 35.40 2.15
480 1428 9.791820 CAAAGTTTGAGCATATTTGATATCACA 57.208 29.630 10.19 0.00 33.69 3.58
554 1502 5.824097 TGTAGGGACACCAAGAAGTTAAAAC 59.176 40.000 0.00 0.00 40.13 2.43
696 1845 9.864034 CATAAAAGTCAGCCAATTTACGTATAG 57.136 33.333 0.00 0.00 0.00 1.31
775 1925 9.017669 CAAAGCTCATCTCTATGTTAATTTTGC 57.982 33.333 0.00 0.00 34.50 3.68
815 1965 5.163513 GGAACCTGTTCGTTCGTTCTATAA 58.836 41.667 4.09 0.00 42.57 0.98
816 1966 5.809051 GGAACCTGTTCGTTCGTTCTATAAT 59.191 40.000 4.09 0.00 42.57 1.28
817 1967 6.974622 GGAACCTGTTCGTTCGTTCTATAATA 59.025 38.462 4.09 0.00 42.57 0.98
818 1968 7.043788 GGAACCTGTTCGTTCGTTCTATAATAC 60.044 40.741 4.09 0.00 42.57 1.89
819 1969 7.093322 ACCTGTTCGTTCGTTCTATAATACT 57.907 36.000 0.00 0.00 0.00 2.12
820 1970 6.971184 ACCTGTTCGTTCGTTCTATAATACTG 59.029 38.462 0.00 0.00 0.00 2.74
821 1971 6.971184 CCTGTTCGTTCGTTCTATAATACTGT 59.029 38.462 0.00 0.00 0.00 3.55
822 1972 8.124823 CCTGTTCGTTCGTTCTATAATACTGTA 58.875 37.037 0.00 0.00 0.00 2.74
823 1973 8.826546 TGTTCGTTCGTTCTATAATACTGTAC 57.173 34.615 0.00 0.00 0.00 2.90
824 1974 8.668353 TGTTCGTTCGTTCTATAATACTGTACT 58.332 33.333 0.00 0.00 0.00 2.73
827 1977 9.750125 TCGTTCGTTCTATAATACTGTACTAGA 57.250 33.333 0.00 0.00 0.00 2.43
877 2027 2.291024 GGAGCGGGGATCTCTATGTCTA 60.291 54.545 0.00 0.00 0.00 2.59
903 2053 4.327680 GAGAGGCAGGATTTAAGTTGTGT 58.672 43.478 0.00 0.00 0.00 3.72
1675 2889 2.284699 AGGTCTCCCTTGGGGTCG 60.285 66.667 5.78 0.00 44.74 4.79
1710 2924 2.431683 GTGACTCTGGCCCTGCAA 59.568 61.111 0.00 0.00 0.00 4.08
2050 3273 2.032634 GGCTTCACGAACGATGGCA 61.033 57.895 0.14 0.00 36.15 4.92
2276 3519 2.819595 CCCGGACGCATTCTGTGG 60.820 66.667 0.73 0.00 30.87 4.17
2508 3752 3.916392 CTTCGCCTTCGACGGTGCT 62.916 63.158 16.22 0.00 45.43 4.40
2751 3995 1.944177 AGGCTAGAGTTTGCTCCTCA 58.056 50.000 0.00 0.00 42.59 3.86
2870 4190 7.811482 TTGTGGTTTACCCCTCTATTAGTTA 57.189 36.000 0.00 0.00 34.29 2.24
2965 5302 0.307760 GTCACGCCTCTGTTTGGTTG 59.692 55.000 0.00 0.00 0.00 3.77
3018 5356 0.109723 TACTTGTTTTGGGCGAGCCT 59.890 50.000 14.33 0.00 36.10 4.58
3022 5360 0.109723 TGTTTTGGGCGAGCCTAACT 59.890 50.000 12.50 0.00 36.28 2.24
3088 5426 5.412286 GCCAAATTTGCTGGATGTAAACAAT 59.588 36.000 12.92 0.00 35.85 2.71
3091 5429 8.442384 CCAAATTTGCTGGATGTAAACAATTAC 58.558 33.333 12.92 0.00 38.02 1.89
3123 5461 5.393352 GCTCATAATGGCATTTCAGTTGTCA 60.393 40.000 19.21 0.00 32.45 3.58
3255 5628 4.307032 AAACTGCATAACATGGGACTCT 57.693 40.909 0.00 0.00 0.00 3.24
3282 5656 5.878116 CGAGGTAAAATGTGTAGGGAAATCA 59.122 40.000 0.00 0.00 0.00 2.57
3355 5729 6.757947 TGAGCAGTTCCATCTTTTTCAAAAAG 59.242 34.615 15.46 15.46 0.00 2.27
3360 5735 5.289083 TCCATCTTTTTCAAAAAGGGGTG 57.711 39.130 20.23 15.86 0.00 4.61
3405 5781 0.767375 ATCATACCCGGCTTCTGCAT 59.233 50.000 0.00 0.00 41.91 3.96
3438 5814 4.003648 CACACTGTCAAATAAGGTCCTCC 58.996 47.826 0.00 0.00 0.00 4.30
3443 5819 3.244770 TGTCAAATAAGGTCCTCCCACAC 60.245 47.826 0.00 0.00 34.66 3.82
3488 5870 7.063544 GCGAAATACAAAGAGACATGTAGAGTT 59.936 37.037 0.00 0.00 35.64 3.01
3496 5878 9.737427 CAAAGAGACATGTAGAGTTCGTATAAT 57.263 33.333 0.00 0.00 0.00 1.28
3502 5884 7.948357 ACATGTAGAGTTCGTATAATGCCTAA 58.052 34.615 0.00 0.00 0.00 2.69
3515 5897 3.331002 GCCTAAAGCATAGGGGAGC 57.669 57.895 15.17 0.36 42.97 4.70
3517 5899 1.133792 GCCTAAAGCATAGGGGAGCAA 60.134 52.381 15.17 0.00 42.97 3.91
3518 5900 2.576615 CCTAAAGCATAGGGGAGCAAC 58.423 52.381 7.53 0.00 0.00 4.17
3519 5901 2.576615 CTAAAGCATAGGGGAGCAACC 58.423 52.381 0.00 0.00 38.08 3.77
3531 5913 2.225467 GGAGCAACCCTAAGATCATGC 58.775 52.381 0.00 0.00 0.00 4.06
3539 5921 2.289945 CCCTAAGATCATGCTGCTACCC 60.290 54.545 0.00 0.00 0.00 3.69
3542 5924 4.223700 CCTAAGATCATGCTGCTACCCATA 59.776 45.833 0.00 0.00 0.00 2.74
3562 5944 5.938125 CCATATTGGGTAAAAGTATCCCTCG 59.062 44.000 0.00 0.00 41.58 4.63
3568 5951 5.721000 TGGGTAAAAGTATCCCTCGTTTAGA 59.279 40.000 0.00 0.00 41.58 2.10
3576 5959 6.807789 AGTATCCCTCGTTTAGACTTCAATC 58.192 40.000 0.00 0.00 0.00 2.67
3606 5989 1.749634 CCTCCGTAAACAGGTCTCGAT 59.250 52.381 0.00 0.00 0.00 3.59
3611 5994 3.436496 CGTAAACAGGTCTCGATTCTCC 58.564 50.000 0.00 0.00 0.00 3.71
3623 6006 1.466866 CGATTCTCCACGCGTTGTAGA 60.467 52.381 10.22 10.13 0.00 2.59
3647 6030 3.522553 GGACCATAAACGAAGAGTCCTG 58.477 50.000 0.00 0.00 40.51 3.86
3648 6031 3.194968 GGACCATAAACGAAGAGTCCTGA 59.805 47.826 0.00 0.00 40.51 3.86
3649 6032 4.174762 GACCATAAACGAAGAGTCCTGAC 58.825 47.826 0.00 0.00 0.00 3.51
3651 6034 4.223032 ACCATAAACGAAGAGTCCTGACAT 59.777 41.667 0.00 0.00 0.00 3.06
3654 6037 6.642950 CCATAAACGAAGAGTCCTGACATATC 59.357 42.308 0.00 0.00 0.00 1.63
3672 6055 5.011023 ACATATCTGTCGATAACCTGCATCA 59.989 40.000 0.00 0.00 35.84 3.07
3690 6073 7.010923 CCTGCATCAGAGAAGTACTTTTATCAC 59.989 40.741 10.02 0.00 32.44 3.06
3738 6121 7.318141 AGCCAAAGTGATCAAATAATGACAAG 58.682 34.615 0.00 0.00 41.93 3.16
3740 6123 6.252015 CCAAAGTGATCAAATAATGACAAGCG 59.748 38.462 0.00 0.00 41.93 4.68
3743 6126 5.124457 AGTGATCAAATAATGACAAGCGCTT 59.876 36.000 18.98 18.98 41.93 4.68
3748 6131 4.989279 AATAATGACAAGCGCTTCCATT 57.011 36.364 32.18 32.18 31.91 3.16
3749 6132 2.927553 AATGACAAGCGCTTCCATTC 57.072 45.000 28.05 19.63 0.00 2.67
3756 6139 0.743701 AGCGCTTCCATTCTGAGCAG 60.744 55.000 2.64 0.00 36.22 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 960 2.083774 CATCAACAACACCCATACGCT 58.916 47.619 0.00 0.00 0.00 5.07
81 1028 2.806244 GGTGACTATGACACACAACACC 59.194 50.000 0.00 0.00 39.65 4.16
199 1146 6.566187 CGTCTATAGCAAGCACTAGATACGTT 60.566 42.308 0.00 0.00 32.54 3.99
262 1209 1.284841 CCCCTTGGCCTCCAGAGAAT 61.285 60.000 3.32 0.00 33.81 2.40
334 1282 7.865875 ATCAGATGATATTTCTCGACGAAAG 57.134 36.000 13.08 0.00 44.29 2.62
365 1313 6.660722 CATTGATTTTTGTTTCCCATGTGTG 58.339 36.000 0.00 0.00 0.00 3.82
415 1363 3.634448 TCGAGGAGCTCTATCCAAGAAAG 59.366 47.826 14.64 0.00 42.26 2.62
554 1502 7.038659 GCACTATTATATGCTTAGAGAGTGGG 58.961 42.308 15.82 1.33 38.84 4.61
686 1835 8.519492 ACGAAAACACTTTAGCTATACGTAAA 57.481 30.769 0.00 0.00 0.00 2.01
696 1845 4.561213 AGTGCAAAACGAAAACACTTTAGC 59.439 37.500 0.00 0.00 38.38 3.09
720 1869 9.616156 TTTTTGTAGGAGTGACAAACAACTATA 57.384 29.630 0.63 0.00 44.33 1.31
775 1925 0.315251 TCCAGCGTGAGTGAAGTCAG 59.685 55.000 0.00 0.00 0.00 3.51
828 1978 9.961265 CATGTGTAACTTCCTTAATCGAGTATA 57.039 33.333 0.00 0.00 38.04 1.47
829 1979 8.692710 TCATGTGTAACTTCCTTAATCGAGTAT 58.307 33.333 0.00 0.00 38.04 2.12
830 1980 8.058667 TCATGTGTAACTTCCTTAATCGAGTA 57.941 34.615 0.00 0.00 38.04 2.59
831 1981 6.931838 TCATGTGTAACTTCCTTAATCGAGT 58.068 36.000 0.00 0.00 38.04 4.18
838 1988 4.381612 CGCTCCTCATGTGTAACTTCCTTA 60.382 45.833 0.00 0.00 38.04 2.69
848 1998 1.690219 GATCCCCGCTCCTCATGTGT 61.690 60.000 0.00 0.00 0.00 3.72
877 2027 4.870021 ACTTAAATCCTGCCTCTCCATT 57.130 40.909 0.00 0.00 0.00 3.16
1675 2889 4.477975 CTGGGAGACGACGCCGAC 62.478 72.222 0.00 0.00 39.50 4.79
1885 3099 1.792118 AAAAGGAACAAGCCGCCGAC 61.792 55.000 0.00 0.00 0.00 4.79
1892 3106 0.241213 GGAGCGGAAAAGGAACAAGC 59.759 55.000 0.00 0.00 0.00 4.01
2751 3995 7.028131 ACCATCATTCCTAATAATCCTCCTCT 58.972 38.462 0.00 0.00 0.00 3.69
2768 4012 4.949856 GGAAACATGAGTGGTACCATCATT 59.050 41.667 25.11 17.33 31.38 2.57
2867 4187 8.807581 GCTGCCAAAACATGACTATTATTTAAC 58.192 33.333 0.00 0.00 0.00 2.01
2870 4190 7.174107 AGCTGCCAAAACATGACTATTATTT 57.826 32.000 0.00 0.00 0.00 1.40
2889 5224 0.937304 TCGTCTCACAAACAAGCTGC 59.063 50.000 0.00 0.00 0.00 5.25
2945 5282 1.157870 AACCAAACAGAGGCGTGACG 61.158 55.000 0.00 0.00 0.00 4.35
2965 5302 1.178534 TTGTAGCCTTGCAGGTTGCC 61.179 55.000 0.00 0.00 44.23 4.52
3123 5461 7.175293 GGAGGAGATAAGAACTGTCGTACATAT 59.825 40.741 0.00 0.00 0.00 1.78
3185 5523 2.615493 CCTCGAATTGGCAACTAGTGGT 60.615 50.000 0.00 0.00 37.61 4.16
3246 5619 2.750141 TTACCTCGCTAGAGTCCCAT 57.250 50.000 0.00 0.00 42.86 4.00
3255 5628 4.025360 TCCCTACACATTTTACCTCGCTA 58.975 43.478 0.00 0.00 0.00 4.26
3282 5656 2.442236 ATGAGGCGATTGTCCCAAAT 57.558 45.000 0.00 0.00 0.00 2.32
3378 5753 6.438763 CAGAAGCCGGGTATGATTTTAAATC 58.561 40.000 6.57 10.47 0.00 2.17
3385 5760 0.546122 TGCAGAAGCCGGGTATGATT 59.454 50.000 19.76 0.00 41.13 2.57
3386 5761 0.767375 ATGCAGAAGCCGGGTATGAT 59.233 50.000 19.76 9.38 41.13 2.45
3387 5762 1.419381 TATGCAGAAGCCGGGTATGA 58.581 50.000 19.76 7.79 41.13 2.15
3388 5763 2.254546 TTATGCAGAAGCCGGGTATG 57.745 50.000 6.57 10.71 41.13 2.39
3389 5764 3.508845 AATTATGCAGAAGCCGGGTAT 57.491 42.857 6.57 0.00 41.13 2.73
3390 5765 4.101898 TCTTAATTATGCAGAAGCCGGGTA 59.898 41.667 6.57 0.00 41.13 3.69
3391 5766 3.118038 TCTTAATTATGCAGAAGCCGGGT 60.118 43.478 0.00 0.00 41.13 5.28
3392 5767 3.476552 TCTTAATTATGCAGAAGCCGGG 58.523 45.455 2.18 0.00 41.13 5.73
3438 5814 9.111702 CGCCATTTTTAATTTTTATTTGTGTGG 57.888 29.630 0.00 0.00 0.00 4.17
3460 5836 4.323417 ACATGTCTCTTTGTATTTCGCCA 58.677 39.130 0.00 0.00 0.00 5.69
3461 5837 4.946784 ACATGTCTCTTTGTATTTCGCC 57.053 40.909 0.00 0.00 0.00 5.54
3513 5895 2.928334 CAGCATGATCTTAGGGTTGCT 58.072 47.619 0.00 0.00 39.69 3.91
3514 5896 1.336125 GCAGCATGATCTTAGGGTTGC 59.664 52.381 0.00 0.00 39.69 4.17
3515 5897 2.928334 AGCAGCATGATCTTAGGGTTG 58.072 47.619 0.00 0.00 39.69 3.77
3517 5899 2.370189 GGTAGCAGCATGATCTTAGGGT 59.630 50.000 0.00 0.00 39.69 4.34
3518 5900 2.289945 GGGTAGCAGCATGATCTTAGGG 60.290 54.545 0.00 0.00 39.69 3.53
3519 5901 2.369860 TGGGTAGCAGCATGATCTTAGG 59.630 50.000 0.00 0.00 39.69 2.69
3539 5921 6.531021 ACGAGGGATACTTTTACCCAATATG 58.469 40.000 0.00 0.00 45.43 1.78
3542 5924 5.446260 AACGAGGGATACTTTTACCCAAT 57.554 39.130 0.00 0.00 45.43 3.16
3553 5935 5.686397 CGATTGAAGTCTAAACGAGGGATAC 59.314 44.000 0.00 0.00 0.00 2.24
3562 5944 6.578691 GTGTGTACACGATTGAAGTCTAAAC 58.421 40.000 20.61 4.73 37.10 2.01
3611 5994 0.456312 GGTCCTCTCTACAACGCGTG 60.456 60.000 14.98 10.05 0.00 5.34
3623 6006 3.447944 GGACTCTTCGTTTATGGTCCTCT 59.552 47.826 0.00 0.00 39.79 3.69
3647 6030 4.871513 TGCAGGTTATCGACAGATATGTC 58.128 43.478 10.51 10.51 38.95 3.06
3648 6031 4.937201 TGCAGGTTATCGACAGATATGT 57.063 40.909 0.00 0.00 38.95 2.29
3649 6032 5.473039 TGATGCAGGTTATCGACAGATATG 58.527 41.667 0.00 0.00 38.95 1.78
3651 6034 4.827284 TCTGATGCAGGTTATCGACAGATA 59.173 41.667 0.00 0.00 33.83 1.98
3654 6037 3.067320 TCTCTGATGCAGGTTATCGACAG 59.933 47.826 0.00 0.00 31.51 3.51
3710 6093 8.407832 TGTCATTATTTGATCACTTTGGCTATG 58.592 33.333 0.00 0.00 36.54 2.23
3715 6098 6.252015 CGCTTGTCATTATTTGATCACTTTGG 59.748 38.462 0.00 0.00 36.54 3.28
3721 6104 5.449041 GGAAGCGCTTGTCATTATTTGATCA 60.449 40.000 30.47 0.00 36.54 2.92
3724 6107 3.755905 TGGAAGCGCTTGTCATTATTTGA 59.244 39.130 30.47 0.00 0.00 2.69
3738 6121 1.023513 ACTGCTCAGAATGGAAGCGC 61.024 55.000 0.00 0.00 36.16 5.92
3740 6123 2.709213 AGAACTGCTCAGAATGGAAGC 58.291 47.619 3.60 0.00 36.16 3.86
3743 6126 6.398234 GTAGATAGAACTGCTCAGAATGGA 57.602 41.667 3.60 0.00 36.16 3.41


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

AutoCloner maintained by Alex Coulton.