Multiple sequence alignment - TraesCS4B01G101100

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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 TraesCS4B01G101100 chr4B 100.000 3710 0 0 1 3710 106822311 106826020 0.000000e+00 6852
1 TraesCS4B01G101100 chr4D 92.849 3412 174 36 68 3432 74354178 74357566 0.000000e+00 4885
2 TraesCS4B01G101100 chr4D 94.667 150 6 2 3562 3710 74357811 74357959 8.010000e-57 231
3 TraesCS4B01G101100 chr4D 87.591 137 15 2 3432 3567 74357640 74357775 1.380000e-34 158
4 TraesCS4B01G101100 chr4A 93.956 1969 105 3 748 2710 513330267 513328307 0.000000e+00 2964
5 TraesCS4B01G101100 chr4A 90.751 692 42 13 68 752 513340550 513339874 0.000000e+00 904
6 TraesCS4B01G101100 chr4A 84.105 497 46 16 2708 3196 513328000 513327529 2.030000e-122 449
7 TraesCS4B01G101100 chr4A 87.313 134 15 2 3432 3563 513327293 513327160 6.420000e-33 152
8 TraesCS4B01G101100 chr4A 98.630 73 0 1 1 73 31621138 31621067 1.080000e-25 128
9 TraesCS4B01G101100 chr4A 97.333 75 1 1 1 74 168769973 168770047 3.890000e-25 126
10 TraesCS4B01G101100 chr4A 97.297 74 2 0 1 74 710743599 710743526 3.890000e-25 126
11 TraesCS4B01G101100 chr7B 100.000 70 0 0 1 70 489828555 489828624 3.010000e-26 130
12 TraesCS4B01G101100 chrUn 97.333 75 2 0 1 75 71016543 71016469 1.080000e-25 128
13 TraesCS4B01G101100 chr5B 97.333 75 2 0 1 75 577021679 577021605 1.080000e-25 128
14 TraesCS4B01G101100 chr3A 98.630 73 0 1 1 72 646739177 646739249 1.080000e-25 128
15 TraesCS4B01G101100 chr2D 95.122 82 2 2 1 82 646589582 646589661 1.080000e-25 128
16 TraesCS4B01G101100 chr6A 94.937 79 4 0 1 79 563561500 563561422 1.400000e-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 TraesCS4B01G101100 chr4B 106822311 106826020 3709 False 6852.000000 6852 100.000000 1 3710 1 chr4B.!!$F1 3709
1 TraesCS4B01G101100 chr4D 74354178 74357959 3781 False 1758.000000 4885 91.702333 68 3710 3 chr4D.!!$F1 3642
2 TraesCS4B01G101100 chr4A 513327160 513330267 3107 True 1188.333333 2964 88.458000 748 3563 3 chr4A.!!$R4 2815
3 TraesCS4B01G101100 chr4A 513339874 513340550 676 True 904.000000 904 90.751000 68 752 1 chr4A.!!$R2 684

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
21 22 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.0 23.81 13.97 37.5 3.46 F
1061 1077 0.667993 TTGCTAGCGCTGCTGTTTTT 59.332 45.0 22.90 0.00 40.1 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1824 0.031994 GAGGCTGCGAGAGAATCCTC 59.968 60.0 0.00 0.0 39.72 3.71 R
2729 3059 0.318955 GTTTGGCTTGCAGCACGAAT 60.319 50.0 2.37 0.0 44.75 3.34 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
17 18 2.833957 ACCCAAAGTGGTCGGACC 59.166 61.111 20.36 20.36 35.17 4.46
18 19 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
19 20 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
20 21 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
21 22 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
22 23 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
23 24 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
24 25 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
25 26 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
26 27 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
27 28 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
28 29 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
29 30 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
30 31 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
31 32 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
32 33 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
33 34 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
34 35 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
35 36 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
56 57 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
57 58 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
58 59 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
59 60 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
60 61 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
61 62 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
62 63 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
63 64 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
64 65 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
208 212 8.695456 AGCTCATTTTCTTTCCTTTAGTTCAAA 58.305 29.630 0.00 0.00 0.00 2.69
226 230 8.063200 AGTTCAAAGGTAAAGTAGCAAAGTTT 57.937 30.769 0.00 0.00 34.96 2.66
379 384 3.035363 TCCTAATGGTGGACGCATCTTA 58.965 45.455 0.00 0.00 34.23 2.10
416 422 1.210931 CCAAGGCATGTCAGCAACG 59.789 57.895 0.00 0.00 35.83 4.10
431 437 2.939103 AGCAACGTTAATCTCATCAGCC 59.061 45.455 0.00 0.00 0.00 4.85
451 457 5.784750 GCCATTGCTTAATTTCCTTGAAC 57.215 39.130 0.00 0.00 33.53 3.18
489 496 9.418045 TCAAAATAGTTGCTTAAAAATACAGGC 57.582 29.630 0.00 0.00 0.00 4.85
493 500 6.588719 AGTTGCTTAAAAATACAGGCATGA 57.411 33.333 4.84 0.00 0.00 3.07
517 524 7.707464 TGATAAGAAAATATGTAGAAACGCCGA 59.293 33.333 0.00 0.00 0.00 5.54
533 540 3.427193 ACGCCGAAATAATTGTGCAAAAC 59.573 39.130 0.00 0.00 0.00 2.43
535 542 4.091220 CGCCGAAATAATTGTGCAAAACAT 59.909 37.500 0.00 0.00 38.99 2.71
555 562 7.506328 AACATAGGTTTACTTCCAGAACAAC 57.494 36.000 0.00 0.00 31.83 3.32
557 565 6.710744 ACATAGGTTTACTTCCAGAACAACAG 59.289 38.462 0.00 0.00 0.00 3.16
559 567 5.941788 AGGTTTACTTCCAGAACAACAGAT 58.058 37.500 0.00 0.00 0.00 2.90
560 568 6.365520 AGGTTTACTTCCAGAACAACAGATT 58.634 36.000 0.00 0.00 0.00 2.40
570 578 5.342433 CAGAACAACAGATTTTGAGCACAA 58.658 37.500 0.00 0.00 0.00 3.33
612 620 9.262358 GGTTTATTTTTATGTTTAGTGTTGGCA 57.738 29.630 0.00 0.00 0.00 4.92
887 896 5.522097 GCTACTTTCTCTACCATTGCTTCTC 59.478 44.000 0.00 0.00 0.00 2.87
902 911 3.452627 TGCTTCTCCTACCCATCTTCTTC 59.547 47.826 0.00 0.00 0.00 2.87
972 988 2.620112 CCTGCAAACAGCTGACCCG 61.620 63.158 23.35 6.77 44.15 5.28
997 1013 7.041644 CGATAGGTTACAGAAGAGAAGAGGTAG 60.042 44.444 0.00 0.00 0.00 3.18
1061 1077 0.667993 TTGCTAGCGCTGCTGTTTTT 59.332 45.000 22.90 0.00 40.10 1.94
1078 1094 5.867166 TGTTTTTCTTGCTGTTTGATTTGC 58.133 33.333 0.00 0.00 0.00 3.68
1116 1132 0.874390 CTCTGCGGCTAAACAAAGCA 59.126 50.000 0.00 0.00 44.64 3.91
1240 1256 0.679505 TTGCTCTGTGCCGTCTAACT 59.320 50.000 0.00 0.00 42.00 2.24
1402 1418 2.771762 AGCTCTCCTCATGCCCCC 60.772 66.667 0.00 0.00 0.00 5.40
1516 1532 3.822735 TGATTTCTCCTTCAGTTTGCTGG 59.177 43.478 0.00 0.00 42.78 4.85
1576 1592 8.041323 CCAGATTAAGAAGCTTGAACCTTAGTA 58.959 37.037 2.10 0.00 0.00 1.82
1837 1853 1.227380 CGCAGCCTCTATCGCCTTT 60.227 57.895 0.00 0.00 0.00 3.11
1838 1854 1.493950 CGCAGCCTCTATCGCCTTTG 61.494 60.000 0.00 0.00 0.00 2.77
1848 1864 1.961180 ATCGCCTTTGTCTCGGAGGG 61.961 60.000 4.96 0.00 0.00 4.30
1858 1874 0.541998 TCTCGGAGGGAACTTGCTCA 60.542 55.000 4.96 0.00 44.43 4.26
1859 1875 0.108424 CTCGGAGGGAACTTGCTCAG 60.108 60.000 0.00 0.00 44.43 3.35
1863 1879 0.957888 GAGGGAACTTGCTCAGTGGC 60.958 60.000 0.00 0.00 44.43 5.01
1866 1882 1.578423 GAACTTGCTCAGTGGCAGC 59.422 57.895 6.43 2.10 43.39 5.25
1924 1945 8.097038 TGTCTTATCTTGAGCTGAACAATAACT 58.903 33.333 0.00 0.00 0.00 2.24
1931 1952 5.865085 TGAGCTGAACAATAACTACTTGGT 58.135 37.500 0.00 0.00 0.00 3.67
1973 1994 0.453390 GGCAGATGCAGTAAGTTGGC 59.547 55.000 7.19 0.00 44.36 4.52
2004 2025 1.412079 TGGCAAGCAACCAGTTGAAT 58.588 45.000 14.56 0.00 42.93 2.57
2044 2065 1.003118 TCGGCAAACTTGATAGCCTGT 59.997 47.619 0.00 0.00 44.85 4.00
2119 2140 5.947228 TGTCAATCTGGTGAACTTGAATC 57.053 39.130 0.00 0.00 30.06 2.52
2205 2226 5.525378 ACGGCTTTCAAACATAAATTTGCAA 59.475 32.000 0.00 0.00 39.08 4.08
2225 2246 1.237285 GGCAACAAGATCACTGGCGT 61.237 55.000 0.00 0.00 0.00 5.68
2382 2403 6.833933 GTGGGTCTATTCCTTCAAATATTGGT 59.166 38.462 0.00 0.00 0.00 3.67
2473 2494 2.584492 AGGTTTGCAAAGCTTGACAC 57.416 45.000 32.52 11.18 43.61 3.67
2478 2499 4.420168 GTTTGCAAAGCTTGACACAGTTA 58.580 39.130 13.26 0.00 0.00 2.24
2499 2520 8.333908 CAGTTAGTGCTTTCTTATAATCAGCTG 58.666 37.037 7.63 7.63 0.00 4.24
2502 2523 6.409704 AGTGCTTTCTTATAATCAGCTGTCA 58.590 36.000 14.67 0.00 0.00 3.58
2570 2591 7.065563 CACAGGAAATCCAGATCTTCTTAACAG 59.934 40.741 1.67 0.00 38.89 3.16
2662 2683 1.336440 CATTTGTGGTTGGCTTCGTCA 59.664 47.619 0.00 0.00 0.00 4.35
2726 3056 3.019564 GTTGAATGGGCAACTAGCTGAT 58.980 45.455 0.00 0.00 43.60 2.90
2729 3059 4.854173 TGAATGGGCAACTAGCTGATTAA 58.146 39.130 0.00 0.00 44.79 1.40
2777 3113 2.877786 CAAGCCATGGATGCACGTAATA 59.122 45.455 18.40 0.00 0.00 0.98
2783 3119 5.175491 GCCATGGATGCACGTAATATTTTTG 59.825 40.000 18.40 0.00 0.00 2.44
2793 3129 6.744082 GCACGTAATATTTTTGTGGTTAGGAC 59.256 38.462 13.12 0.00 0.00 3.85
2891 3227 2.438868 AGGCATTTTCTCCGCAAAAC 57.561 45.000 0.00 0.00 0.00 2.43
2925 3262 5.021033 AGCAGAGTATTCAGATTGTCCTG 57.979 43.478 0.00 0.00 35.55 3.86
2949 3286 3.933332 GGAACATGGTTAGGAAGAGTTCG 59.067 47.826 0.00 0.00 35.86 3.95
3003 3344 7.504924 TTGGACTTCAATTAAGAACAATCGT 57.495 32.000 0.00 0.00 38.67 3.73
3020 3361 1.200716 TCGTTCGGTATTCTCGCAGTT 59.799 47.619 0.00 0.00 0.00 3.16
3027 3368 3.975670 CGGTATTCTCGCAGTTGTAGATC 59.024 47.826 0.00 0.00 0.00 2.75
3028 3369 4.261238 CGGTATTCTCGCAGTTGTAGATCT 60.261 45.833 0.00 0.00 0.00 2.75
3049 3390 1.881973 TGAACAATCAAGACTGCAGGC 59.118 47.619 19.93 16.91 30.99 4.85
3068 3425 2.485124 GGCAAGACTGATCCAGGAGATG 60.485 54.545 0.00 0.00 34.42 2.90
3090 3447 4.082625 TGCTTGAATGTTGGTGCTCTATTG 60.083 41.667 0.00 0.00 0.00 1.90
3093 3450 1.767759 ATGTTGGTGCTCTATTGGCC 58.232 50.000 0.00 0.00 0.00 5.36
3102 3463 2.175284 TGCTCTATTGGCCAATCATCCA 59.825 45.455 33.89 22.35 32.50 3.41
3196 3561 4.842531 TGAAGCAATCAGAGGAATGGTA 57.157 40.909 0.00 0.00 33.72 3.25
3197 3562 4.517285 TGAAGCAATCAGAGGAATGGTAC 58.483 43.478 0.00 0.00 33.72 3.34
3224 3589 1.920762 GCTACGAGCAACGCAGATC 59.079 57.895 7.54 0.00 46.94 2.75
3260 3625 2.076863 CACACGGAAGGCTAAGAAAGG 58.923 52.381 0.00 0.00 0.00 3.11
3281 3646 1.147153 GCACCTACCTCATCCTGCC 59.853 63.158 0.00 0.00 0.00 4.85
3304 3669 3.822192 CACGTCGCCGGATCAGGA 61.822 66.667 16.86 0.00 38.78 3.86
3305 3670 3.823330 ACGTCGCCGGATCAGGAC 61.823 66.667 16.86 4.88 38.78 3.85
3306 3671 4.907034 CGTCGCCGGATCAGGACG 62.907 72.222 16.86 17.37 44.92 4.79
3311 3676 4.873129 CCGGATCAGGACGGCGTG 62.873 72.222 21.19 4.09 43.96 5.34
3312 3677 3.822192 CGGATCAGGACGGCGTGA 61.822 66.667 21.19 17.22 42.43 4.35
3313 3678 2.105128 GGATCAGGACGGCGTGAG 59.895 66.667 21.19 6.98 41.64 3.51
3422 3804 1.266989 GAAAGGAAGGCCGAAAGTGTG 59.733 52.381 0.00 0.00 39.96 3.82
3512 3968 3.793144 CCGCAGAACTCGCAAGGC 61.793 66.667 0.00 0.00 38.47 4.35
3563 4021 1.959985 CACGCACTCCATCTATCCTCT 59.040 52.381 0.00 0.00 0.00 3.69
3567 4067 2.029470 GCACTCCATCTATCCTCTTCCG 60.029 54.545 0.00 0.00 0.00 4.30
3580 4080 3.704231 CTTCCGGTGGGGATGCCAG 62.704 68.421 5.30 0.00 46.62 4.85
3678 4178 1.339535 TGTTATGGCGCCTTGTCATCA 60.340 47.619 29.70 14.15 39.09 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
1 2 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2 3 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3 4 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
4 5 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
5 6 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
6 7 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
7 8 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
8 9 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
9 10 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
10 11 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
11 12 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
12 13 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
13 14 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
14 15 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
15 16 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
16 17 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
17 18 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
18 19 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
30 31 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
33 34 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
34 35 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
35 36 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
36 37 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
38 39 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
39 40 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
40 41 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
41 42 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
42 43 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
43 44 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
44 45 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
45 46 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
46 47 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
57 58 1.064389 ACTGAAGATTAAGGGCAGCCC 60.064 52.381 24.90 24.90 45.90 5.19
58 59 2.019984 CACTGAAGATTAAGGGCAGCC 58.980 52.381 1.26 1.26 0.00 4.85
59 60 1.403323 GCACTGAAGATTAAGGGCAGC 59.597 52.381 0.00 0.00 42.61 5.25
60 61 2.019984 GGCACTGAAGATTAAGGGCAG 58.980 52.381 6.51 0.00 44.97 4.85
61 62 1.635487 AGGCACTGAAGATTAAGGGCA 59.365 47.619 6.51 0.00 44.97 5.36
62 63 2.426842 AGGCACTGAAGATTAAGGGC 57.573 50.000 0.00 0.00 42.33 5.19
63 64 5.501156 AGTAAAGGCACTGAAGATTAAGGG 58.499 41.667 0.00 0.00 40.86 3.95
64 65 8.451748 GTTTAGTAAAGGCACTGAAGATTAAGG 58.548 37.037 0.00 0.00 40.86 2.69
65 66 8.999431 TGTTTAGTAAAGGCACTGAAGATTAAG 58.001 33.333 0.00 0.00 40.86 1.85
66 67 8.911918 TGTTTAGTAAAGGCACTGAAGATTAA 57.088 30.769 0.00 0.00 40.86 1.40
155 158 1.203050 AGCACCCTTGTGTTGGCTTAT 60.203 47.619 0.00 0.00 44.65 1.73
263 268 4.722361 TGTGTTTCCCAACAGGTTTTAC 57.278 40.909 0.00 0.00 43.83 2.01
431 437 7.816945 ATTCGTTCAAGGAAATTAAGCAATG 57.183 32.000 0.00 0.00 0.00 2.82
451 457 8.452989 AGCAACTATTTTGAGCTAAAAATTCG 57.547 30.769 23.87 17.68 41.29 3.34
489 496 9.599322 GGCGTTTCTACATATTTTCTTATCATG 57.401 33.333 0.00 0.00 0.00 3.07
493 500 8.428186 TTCGGCGTTTCTACATATTTTCTTAT 57.572 30.769 6.85 0.00 0.00 1.73
502 509 7.403421 CACAATTATTTCGGCGTTTCTACATA 58.597 34.615 6.85 0.00 0.00 2.29
533 540 6.934645 TCTGTTGTTCTGGAAGTAAACCTATG 59.065 38.462 0.00 0.00 33.76 2.23
535 542 6.488769 TCTGTTGTTCTGGAAGTAAACCTA 57.511 37.500 0.00 0.00 33.76 3.08
593 601 7.721402 AGTCAATGCCAACACTAAACATAAAA 58.279 30.769 0.00 0.00 0.00 1.52
599 607 5.144359 CGTAAGTCAATGCCAACACTAAAC 58.856 41.667 0.00 0.00 0.00 2.01
605 613 2.147958 GACCGTAAGTCAATGCCAACA 58.852 47.619 0.00 0.00 45.55 3.33
693 701 1.134699 TCATCGGCAAGTGGTCTGATC 60.135 52.381 0.00 0.00 0.00 2.92
887 896 5.307976 TCATATGTGGAAGAAGATGGGTAGG 59.692 44.000 1.90 0.00 0.00 3.18
972 988 7.255346 GCTACCTCTTCTCTTCTGTAACCTATC 60.255 44.444 0.00 0.00 0.00 2.08
997 1013 0.833287 TACCTGCTCTTCTCCATGGC 59.167 55.000 6.96 0.00 0.00 4.40
1025 1041 4.255510 AGCAATAACCCATGGTGAGAAT 57.744 40.909 11.73 0.00 35.34 2.40
1061 1077 2.037901 TGGGCAAATCAAACAGCAAGA 58.962 42.857 0.00 0.00 0.00 3.02
1116 1132 2.887152 GTTTCTCATGGTGCTTTCCTGT 59.113 45.455 0.00 0.00 0.00 4.00
1240 1256 1.001764 CTGCAGATGAACCAGGGCA 60.002 57.895 8.42 0.00 0.00 5.36
1265 1281 1.608717 GCGAGACATGGAGAGGTGGT 61.609 60.000 0.00 0.00 0.00 4.16
1402 1418 1.450134 TGCGCAATCTAGCACCCAG 60.450 57.895 8.16 0.00 38.59 4.45
1516 1532 3.660865 ACTGTTCGTCTACATTTCCACC 58.339 45.455 0.00 0.00 0.00 4.61
1576 1592 3.073946 AGGCTACCACCAAGTGTATTGTT 59.926 43.478 0.00 0.00 0.00 2.83
1808 1824 0.031994 GAGGCTGCGAGAGAATCCTC 59.968 60.000 0.00 0.00 39.72 3.71
1837 1853 0.832135 AGCAAGTTCCCTCCGAGACA 60.832 55.000 0.00 0.00 0.00 3.41
1838 1854 0.108567 GAGCAAGTTCCCTCCGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
1848 1864 1.168407 TGCTGCCACTGAGCAAGTTC 61.168 55.000 0.00 0.00 43.47 3.01
1858 1874 4.437587 GCCTGGGATGCTGCCACT 62.438 66.667 0.00 0.00 30.85 4.00
1859 1875 4.437587 AGCCTGGGATGCTGCCAC 62.438 66.667 0.00 0.00 37.76 5.01
1863 1879 1.147824 AATCGAGCCTGGGATGCTG 59.852 57.895 0.00 0.00 39.69 4.41
1866 1882 0.816825 CACCAATCGAGCCTGGGATG 60.817 60.000 13.75 2.72 37.00 3.51
1924 1945 1.209621 GGTATGCCTCCCACCAAGTA 58.790 55.000 0.00 0.00 32.32 2.24
1973 1994 2.708051 TGCTTGCCAGATTCAAGAGAG 58.292 47.619 6.89 0.00 42.52 3.20
2044 2065 7.873719 TGTTTATTTGGAGTTTCAGAACAGA 57.126 32.000 0.00 0.00 38.26 3.41
2076 2097 4.260985 CAAGTGTGCTTGGTATATGTCCA 58.739 43.478 0.00 0.00 46.17 4.02
2119 2140 5.305585 TGAGTTTTGGCTAAGGTTCAGTAG 58.694 41.667 0.00 0.00 0.00 2.57
2205 2226 0.957395 CGCCAGTGATCTTGTTGCCT 60.957 55.000 0.00 0.00 0.00 4.75
2225 2246 5.241506 GGTGAACTGATTGAAGTTGGAATGA 59.758 40.000 0.00 0.00 40.48 2.57
2382 2403 3.244911 GGATCTCCAGGTCCTTCAAAACA 60.245 47.826 0.00 0.00 35.64 2.83
2473 2494 8.333908 CAGCTGATTATAAGAAAGCACTAACTG 58.666 37.037 8.42 4.43 36.32 3.16
2478 2499 6.409704 TGACAGCTGATTATAAGAAAGCACT 58.590 36.000 23.35 0.00 36.32 4.40
2547 2568 7.264294 ACTGTTAAGAAGATCTGGATTTCCT 57.736 36.000 0.00 0.00 36.82 3.36
2662 2683 4.234170 TCCCATCCCCATAGAAAGAGAT 57.766 45.455 0.00 0.00 0.00 2.75
2726 3056 1.242989 TGGCTTGCAGCACGAATTAA 58.757 45.000 2.37 0.00 44.75 1.40
2729 3059 0.318955 GTTTGGCTTGCAGCACGAAT 60.319 50.000 2.37 0.00 44.75 3.34
2783 3119 7.553044 AGCATTGTTATCTTTAGTCCTAACCAC 59.447 37.037 0.00 0.00 0.00 4.16
2925 3262 4.287766 ACTCTTCCTAACCATGTTCCAC 57.712 45.455 0.00 0.00 0.00 4.02
2949 3286 6.711579 TGTTGTTCGTTGAGTGTTCTTAATC 58.288 36.000 0.00 0.00 0.00 1.75
3003 3344 2.736144 ACAACTGCGAGAATACCGAA 57.264 45.000 0.00 0.00 0.00 4.30
3028 3369 2.294233 GCCTGCAGTCTTGATTGTTCAA 59.706 45.455 13.81 0.00 39.54 2.69
3045 3386 0.907486 TCCTGGATCAGTCTTGCCTG 59.093 55.000 0.00 0.00 0.00 4.85
3047 3388 1.198713 TCTCCTGGATCAGTCTTGCC 58.801 55.000 0.00 0.00 0.00 4.52
3049 3390 2.435069 AGCATCTCCTGGATCAGTCTTG 59.565 50.000 0.00 0.00 31.27 3.02
3068 3425 4.418392 CAATAGAGCACCAACATTCAAGC 58.582 43.478 0.00 0.00 0.00 4.01
3090 3447 1.473788 GGTTGCAATGGATGATTGGCC 60.474 52.381 0.59 0.00 41.74 5.36
3093 3450 3.193903 TGTCAGGTTGCAATGGATGATTG 59.806 43.478 0.59 0.00 43.97 2.67
3102 3463 2.079158 CATCGAGTGTCAGGTTGCAAT 58.921 47.619 0.59 0.00 0.00 3.56
3165 3530 0.529378 GATTGCTTCAGGTTGCAGGG 59.471 55.000 0.00 0.00 40.46 4.45
3196 3561 2.096596 GCTCGTAGCAGTCGTAGGT 58.903 57.895 2.53 0.00 41.89 3.08
3437 3893 1.364269 TCCGGTATGAAACCCCAACT 58.636 50.000 0.00 0.00 46.62 3.16
3513 3969 3.860930 TTTGGGAGGGAACAGCGCC 62.861 63.158 2.29 0.00 0.00 6.53
3515 3971 1.971695 GGTTTGGGAGGGAACAGCG 60.972 63.158 0.00 0.00 0.00 5.18
3516 3972 1.606601 GGGTTTGGGAGGGAACAGC 60.607 63.158 0.00 0.00 0.00 4.40
3517 3973 0.409484 ATGGGTTTGGGAGGGAACAG 59.591 55.000 0.00 0.00 0.00 3.16
3518 3974 0.407918 GATGGGTTTGGGAGGGAACA 59.592 55.000 0.00 0.00 0.00 3.18
3519 3975 0.324368 GGATGGGTTTGGGAGGGAAC 60.324 60.000 0.00 0.00 0.00 3.62
3520 3976 1.858739 CGGATGGGTTTGGGAGGGAA 61.859 60.000 0.00 0.00 0.00 3.97
3522 3978 2.275418 CGGATGGGTTTGGGAGGG 59.725 66.667 0.00 0.00 0.00 4.30
3529 3987 4.733542 CGTGGGGCGGATGGGTTT 62.734 66.667 0.00 0.00 36.85 3.27
3553 4011 1.483307 CCCCACCGGAAGAGGATAGAT 60.483 57.143 9.46 0.00 34.73 1.98
3563 4021 3.727258 CTGGCATCCCCACCGGAA 61.727 66.667 9.46 0.00 46.47 4.30
3594 4094 4.838486 GGAGAGTGCCGCGACGAG 62.838 72.222 8.23 0.00 0.00 4.18
3602 4102 2.010497 GATTTTTCTCCGGAGAGTGCC 58.990 52.381 31.81 18.01 41.26 5.01
3678 4178 2.093128 CGTACCCAAATCTACCAGCCTT 60.093 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.