Multiple sequence alignment - TraesCS7A01G035300

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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 TraesCS7A01G035300 chr7A 100.000 1886 0 0 958 2843 15689615 15687730 0.000000e+00 3483.0
1 TraesCS7A01G035300 chr7A 100.000 705 0 0 1 705 15690572 15689868 0.000000e+00 1303.0
2 TraesCS7A01G035300 chr7A 81.439 1126 167 18 961 2061 15639895 15638787 0.000000e+00 883.0
3 TraesCS7A01G035300 chr7A 89.773 176 12 5 2188 2358 602028169 602027995 1.330000e-53 220.0
4 TraesCS7A01G035300 chr7A 87.952 83 10 0 339 421 16603355 16603437 6.480000e-17 99.0
5 TraesCS7A01G035300 chr7D 94.041 1611 85 6 958 2560 16705156 16703549 0.000000e+00 2433.0
6 TraesCS7A01G035300 chr7D 94.675 676 34 2 30 705 16705873 16705200 0.000000e+00 1048.0
7 TraesCS7A01G035300 chr7D 82.343 1127 159 25 961 2061 16692004 16690892 0.000000e+00 942.0
8 TraesCS7A01G035300 chr7D 93.966 232 13 1 193 423 16705488 16705257 1.620000e-92 350.0
9 TraesCS7A01G035300 chr7D 93.074 231 14 2 418 648 16705710 16705482 1.260000e-88 337.0
10 TraesCS7A01G035300 chr7D 93.023 172 11 1 2606 2777 16703548 16703378 1.690000e-62 250.0
11 TraesCS7A01G035300 chr7D 78.344 314 37 12 416 705 16692357 16692051 1.050000e-39 174.0
12 TraesCS7A01G035300 chr7D 88.750 80 9 0 342 421 17209565 17209644 6.480000e-17 99.0
13 TraesCS7A01G035300 chr4A 92.575 1697 116 6 958 2649 717971814 717973505 0.000000e+00 2427.0
14 TraesCS7A01G035300 chr4A 94.118 663 39 0 35 697 717971104 717971766 0.000000e+00 1009.0
15 TraesCS7A01G035300 chr4A 92.704 233 16 1 193 424 717971486 717971718 4.540000e-88 335.0
16 TraesCS7A01G035300 chr4A 92.641 231 17 0 418 648 717971262 717971492 1.630000e-87 333.0
17 TraesCS7A01G035300 chr4A 84.047 257 30 9 2192 2441 632867341 632867089 1.320000e-58 237.0
18 TraesCS7A01G035300 chr4A 78.387 310 36 13 416 700 718032784 718033087 3.770000e-39 172.0
19 TraesCS7A01G035300 chr4A 89.516 124 13 0 2696 2819 717973502 717973625 1.050000e-34 158.0
20 TraesCS7A01G035300 chr4A 87.500 80 10 0 342 421 717047792 717047713 3.020000e-15 93.5
21 TraesCS7A01G035300 chr3B 82.060 563 73 14 2192 2736 823188021 823188573 3.340000e-124 455.0
22 TraesCS7A01G035300 chr5A 81.261 587 73 17 2192 2764 546233152 546233715 9.350000e-120 440.0
23 TraesCS7A01G035300 chr5A 85.271 258 27 8 2191 2441 677745037 677745290 3.630000e-64 255.0
24 TraesCS7A01G035300 chr1A 85.098 255 27 9 2194 2441 300770371 300770121 1.690000e-62 250.0
25 TraesCS7A01G035300 chr1A 83.984 256 32 7 2192 2441 452048103 452047851 1.320000e-58 237.0
26 TraesCS7A01G035300 chrUn 87.912 182 15 4 2182 2358 67068179 67068358 1.030000e-49 207.0
27 TraesCS7A01G035300 chr3A 100.000 28 0 0 2113 2140 686985489 686985462 5.000000e-03 52.8


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 TraesCS7A01G035300 chr7A 15687730 15690572 2842 True 2393.0 3483 100.0000 1 2843 2 chr7A.!!$R3 2842
1 TraesCS7A01G035300 chr7A 15638787 15639895 1108 True 883.0 883 81.4390 961 2061 1 chr7A.!!$R1 1100
2 TraesCS7A01G035300 chr7D 16703378 16705873 2495 True 883.6 2433 93.7558 30 2777 5 chr7D.!!$R2 2747
3 TraesCS7A01G035300 chr7D 16690892 16692357 1465 True 558.0 942 80.3435 416 2061 2 chr7D.!!$R1 1645
4 TraesCS7A01G035300 chr4A 717971104 717973625 2521 False 852.4 2427 92.3108 35 2819 5 chr4A.!!$F2 2784
5 TraesCS7A01G035300 chr3B 823188021 823188573 552 False 455.0 455 82.0600 2192 2736 1 chr3B.!!$F1 544
6 TraesCS7A01G035300 chr5A 546233152 546233715 563 False 440.0 440 81.2610 2192 2764 1 chr5A.!!$F1 572

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
293 294 1.539827 GTGCGACCCAAACTATGCTTT 59.46 47.619 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2151 0.25077 AAAGCCGGACCCTTCTTGAC 60.251 55.0 5.05 0.0 0.0 3.18 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
22 23 4.520179 ACAAACTCATAGCTCATGATGCA 58.480 39.130 16.20 0.00 42.82 3.96
23 24 5.131067 ACAAACTCATAGCTCATGATGCAT 58.869 37.500 16.20 0.00 42.82 3.96
24 25 5.008712 ACAAACTCATAGCTCATGATGCATG 59.991 40.000 2.46 15.61 42.82 4.06
25 26 3.075148 ACTCATAGCTCATGATGCATGC 58.925 45.455 11.82 11.82 42.82 4.06
26 27 2.073816 TCATAGCTCATGATGCATGCG 58.926 47.619 14.09 0.00 41.18 4.73
27 28 1.804748 CATAGCTCATGATGCATGCGT 59.195 47.619 13.43 13.43 41.18 5.24
28 29 2.818130 TAGCTCATGATGCATGCGTA 57.182 45.000 13.55 1.06 41.18 4.42
58 59 7.189693 TGTACAAGATCAGTTTCACAACATC 57.810 36.000 0.00 0.00 35.05 3.06
151 152 7.041635 TGCATGTTTATCTTACCAATCCATG 57.958 36.000 0.00 0.00 0.00 3.66
195 196 7.169591 TCCAGGGAACAATTAATCGAGTAAAA 58.830 34.615 9.63 0.00 0.00 1.52
198 199 8.458843 CAGGGAACAATTAATCGAGTAAAACAT 58.541 33.333 9.63 0.00 0.00 2.71
273 274 5.528320 ACAGAATGGGTTTTGCAAAAAGATG 59.472 36.000 25.40 17.67 43.62 2.90
293 294 1.539827 GTGCGACCCAAACTATGCTTT 59.460 47.619 0.00 0.00 0.00 3.51
298 299 4.573201 GCGACCCAAACTATGCTTTACATA 59.427 41.667 0.00 0.00 40.38 2.29
336 337 4.572909 TGAGTCATATGCAGGTGATATGC 58.427 43.478 7.03 0.00 44.11 3.14
429 430 8.937634 ATGATCATTTTAAAAAGCATGGAGTC 57.062 30.769 1.18 0.61 0.00 3.36
451 452 7.373493 AGTCTGTGAATGGAAAAGCTAATTTG 58.627 34.615 0.00 0.00 0.00 2.32
489 490 3.418684 AGCTTACAGAATGGGTTTCGT 57.581 42.857 0.00 0.00 43.62 3.85
510 511 5.587043 TCGTAAAAAGATATGCGACCCAAAT 59.413 36.000 0.00 0.00 0.00 2.32
558 582 5.300411 TGATGAGTCATATGCAGGTGATT 57.700 39.130 5.38 3.38 0.00 2.57
577 601 5.342259 GTGATTTGTGCCGAAAAGTACATTC 59.658 40.000 0.00 0.00 0.00 2.67
603 627 5.491070 TGATCACCCAAGATTAGACTTGTG 58.509 41.667 0.00 0.00 43.72 3.33
700 724 3.568007 TGGAATGCAACAAACTAGACCAC 59.432 43.478 0.00 0.00 0.00 4.16
1056 1081 3.142838 GCATCCACCGCCATTGCT 61.143 61.111 0.00 0.00 34.43 3.91
1071 1096 4.581868 CCATTGCTCAATTGGAAACCATT 58.418 39.130 5.42 0.00 31.53 3.16
1078 1103 5.782047 CTCAATTGGAAACCATTTGTAGCA 58.218 37.500 18.39 5.44 42.22 3.49
1111 1136 1.422531 ATGCCAACACCACCAACAAT 58.577 45.000 0.00 0.00 0.00 2.71
1197 1222 1.073763 CCAGTGAGAACACCATTCCCA 59.926 52.381 0.00 0.00 46.99 4.37
1303 1328 2.044650 GCAAGGCCATCCAGAGCA 60.045 61.111 5.01 0.00 33.74 4.26
1349 1374 0.975887 CCCCAACAACAATGGAAGGG 59.024 55.000 0.00 0.00 40.56 3.95
1477 1502 0.913876 GCGACAACAACAACAACAGC 59.086 50.000 0.00 0.00 0.00 4.40
1558 1583 1.034838 GCCATTCCCGCATACACCAA 61.035 55.000 0.00 0.00 0.00 3.67
1572 1597 1.073763 ACACCAATGCAGAAGCCTACA 59.926 47.619 0.00 0.00 41.13 2.74
1643 1668 2.182537 GCAATTCCGCTGCCAAGG 59.817 61.111 0.00 0.00 33.51 3.61
1683 1708 4.460263 AGTCTATCAGGCAACAACAACAA 58.540 39.130 0.00 0.00 41.41 2.83
1741 1787 1.471676 GGATGTCACTTCACGCCCTAG 60.472 57.143 0.00 0.00 0.00 3.02
1743 1789 1.292223 GTCACTTCACGCCCTAGCA 59.708 57.895 0.00 0.00 39.83 3.49
1780 1826 1.357420 ACATCCCTGTACAATGCCCAA 59.643 47.619 6.02 0.00 32.49 4.12
1786 1832 0.891449 TGTACAATGCCCAACCACCG 60.891 55.000 0.00 0.00 0.00 4.94
1823 1869 2.805099 GCATTACCATGACAGCTAGCTC 59.195 50.000 16.15 5.54 31.07 4.09
1860 1906 5.491070 TGCTAGTTGATCAATGTAGCAGTT 58.509 37.500 31.87 9.77 39.09 3.16
1867 1913 5.840715 TGATCAATGTAGCAGTTGCAAAAA 58.159 33.333 0.00 0.00 45.16 1.94
1868 1914 6.457355 TGATCAATGTAGCAGTTGCAAAAAT 58.543 32.000 0.00 0.00 45.16 1.82
1869 1915 7.600960 TGATCAATGTAGCAGTTGCAAAAATA 58.399 30.769 0.00 0.00 45.16 1.40
1895 1942 3.611970 TGTCATGCATCATCATGTGTGA 58.388 40.909 0.00 6.12 43.18 3.58
2111 2162 1.071857 GAACGAAGGGTCAAGAAGGGT 59.928 52.381 0.00 0.00 0.00 4.34
2113 2164 0.036294 CGAAGGGTCAAGAAGGGTCC 60.036 60.000 0.00 0.00 0.00 4.46
2115 2166 1.489560 AAGGGTCAAGAAGGGTCCGG 61.490 60.000 0.00 0.00 0.00 5.14
2124 2175 1.095600 GAAGGGTCCGGCTTTGAATC 58.904 55.000 0.00 0.00 0.00 2.52
2143 2194 3.988379 TCAACAAAGTCATCAACTGGC 57.012 42.857 0.00 0.00 38.58 4.85
2158 2209 2.159382 ACTGGCCTGAAATTACAACGG 58.841 47.619 17.64 0.00 0.00 4.44
2159 2210 2.159382 CTGGCCTGAAATTACAACGGT 58.841 47.619 3.32 0.00 0.00 4.83
2277 2335 9.990868 ATTCCCTATCTAACACCAACTTTAAAT 57.009 29.630 0.00 0.00 0.00 1.40
2371 2432 5.308759 AGTTTACCCCTAACACTAGAAGCAA 59.691 40.000 0.00 0.00 0.00 3.91
2391 2452 6.471146 AGCAACTAAGTCAGATCAAGTTCAT 58.529 36.000 0.00 0.00 0.00 2.57
2423 2484 2.038813 CCGGGCCCAAAATCCCTT 59.961 61.111 24.92 0.00 40.41 3.95
2431 2492 2.617021 GCCCAAAATCCCTTGTACTCGA 60.617 50.000 0.00 0.00 0.00 4.04
2449 2510 2.742372 GAACACCGAGCGGCACAT 60.742 61.111 9.14 0.00 39.32 3.21
2464 2525 4.082523 CATGAGGCGGGTGGTCGT 62.083 66.667 0.00 0.00 0.00 4.34
2465 2526 3.771160 ATGAGGCGGGTGGTCGTC 61.771 66.667 0.00 0.00 34.63 4.20
2472 2533 3.063084 GGGTGGTCGTCTCGCTCT 61.063 66.667 0.00 0.00 0.00 4.09
2528 2589 1.293924 GCTGCACGAGAATATGCTGT 58.706 50.000 0.00 0.00 42.55 4.40
2579 2646 3.073274 TGACAGATCTCAAGGAGACGA 57.927 47.619 0.00 0.00 41.76 4.20
2698 2783 2.764128 GGATGGGAGCGTCTGGGA 60.764 66.667 0.00 0.00 0.00 4.37
2739 2827 4.320494 GGTGGAGTGTTGTTTAGAATGCTG 60.320 45.833 0.00 0.00 0.00 4.41
2747 2835 5.294306 TGTTGTTTAGAATGCTGGATCGATC 59.706 40.000 17.36 17.36 0.00 3.69
2764 2852 4.183686 CCCCTCAAATGCAGCGCG 62.184 66.667 0.00 0.00 0.00 6.86
2777 2865 3.773630 GCGCGCGTACTGCAAAGA 61.774 61.111 32.35 0.00 46.97 2.52
2788 2876 4.388773 CGTACTGCAAAGATAGCTCACAAA 59.611 41.667 0.00 0.00 0.00 2.83
2796 2884 6.264832 CAAAGATAGCTCACAAACACACAAA 58.735 36.000 0.00 0.00 0.00 2.83
2797 2885 6.639632 AAGATAGCTCACAAACACACAAAT 57.360 33.333 0.00 0.00 0.00 2.32
2798 2886 6.005583 AGATAGCTCACAAACACACAAATG 57.994 37.500 0.00 0.00 0.00 2.32
2815 2903 4.463891 ACAAATGGCTCGATTGATTTTCCT 59.536 37.500 2.84 0.00 0.00 3.36
2819 2907 5.097742 TGGCTCGATTGATTTTCCTCTAA 57.902 39.130 0.00 0.00 0.00 2.10
2820 2908 4.876107 TGGCTCGATTGATTTTCCTCTAAC 59.124 41.667 0.00 0.00 0.00 2.34
2821 2909 4.876107 GGCTCGATTGATTTTCCTCTAACA 59.124 41.667 0.00 0.00 0.00 2.41
2822 2910 5.007136 GGCTCGATTGATTTTCCTCTAACAG 59.993 44.000 0.00 0.00 0.00 3.16
2823 2911 5.503194 GCTCGATTGATTTTCCTCTAACAGC 60.503 44.000 0.00 0.00 0.00 4.40
2824 2912 5.487433 TCGATTGATTTTCCTCTAACAGCA 58.513 37.500 0.00 0.00 0.00 4.41
2825 2913 5.582269 TCGATTGATTTTCCTCTAACAGCAG 59.418 40.000 0.00 0.00 0.00 4.24
2826 2914 5.582269 CGATTGATTTTCCTCTAACAGCAGA 59.418 40.000 0.00 0.00 0.00 4.26
2827 2915 6.092670 CGATTGATTTTCCTCTAACAGCAGAA 59.907 38.462 0.00 0.00 0.00 3.02
2828 2916 6.560253 TTGATTTTCCTCTAACAGCAGAAC 57.440 37.500 0.00 0.00 0.00 3.01
2829 2917 4.690748 TGATTTTCCTCTAACAGCAGAACG 59.309 41.667 0.00 0.00 0.00 3.95
2830 2918 4.330944 TTTTCCTCTAACAGCAGAACGA 57.669 40.909 0.00 0.00 0.00 3.85
2831 2919 3.577649 TTCCTCTAACAGCAGAACGAG 57.422 47.619 0.00 0.00 0.00 4.18
2832 2920 1.202582 TCCTCTAACAGCAGAACGAGC 59.797 52.381 0.00 0.00 0.00 5.03
2833 2921 1.067565 CCTCTAACAGCAGAACGAGCA 60.068 52.381 0.00 0.00 0.00 4.26
2834 2922 2.417924 CCTCTAACAGCAGAACGAGCAT 60.418 50.000 0.00 0.00 0.00 3.79
2835 2923 2.602211 CTCTAACAGCAGAACGAGCATG 59.398 50.000 0.00 0.00 0.00 4.06
2836 2924 1.061711 CTAACAGCAGAACGAGCATGC 59.938 52.381 10.51 10.51 40.29 4.06
2837 2925 1.904852 AACAGCAGAACGAGCATGCG 61.905 55.000 13.01 0.84 44.64 4.73
2838 2926 3.494336 AGCAGAACGAGCATGCGC 61.494 61.111 13.01 12.42 44.64 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.952370 ATGTACGCATGCATCATGAGCTATGA 62.952 42.308 19.57 7.89 43.55 2.15
7 8 1.804748 ACGCATGCATCATGAGCTATG 59.195 47.619 19.57 15.71 43.55 2.23
8 9 2.180432 ACGCATGCATCATGAGCTAT 57.820 45.000 19.57 7.19 43.55 2.97
9 10 2.224018 TGTACGCATGCATCATGAGCTA 60.224 45.455 19.57 5.65 43.55 3.32
10 11 1.224075 GTACGCATGCATCATGAGCT 58.776 50.000 19.57 0.00 43.55 4.09
11 12 0.939419 TGTACGCATGCATCATGAGC 59.061 50.000 19.57 5.90 43.55 4.26
12 13 2.159037 GGATGTACGCATGCATCATGAG 59.841 50.000 19.57 9.57 46.61 2.90
13 14 2.145536 GGATGTACGCATGCATCATGA 58.854 47.619 19.57 0.00 46.61 3.07
14 15 2.148768 AGGATGTACGCATGCATCATG 58.851 47.619 19.57 2.94 46.61 3.07
15 16 2.148768 CAGGATGTACGCATGCATCAT 58.851 47.619 19.57 17.24 46.61 2.45
16 17 1.585297 CAGGATGTACGCATGCATCA 58.415 50.000 19.57 13.21 46.61 3.07
27 28 7.256154 TGTGAAACTGATCTTGTACAGGATGTA 60.256 37.037 23.71 12.04 44.50 2.29
146 147 8.519526 GGAACTGATTTTGTAATGTTACATGGA 58.480 33.333 0.00 0.00 42.66 3.41
151 152 7.175990 TCCCTGGAACTGATTTTGTAATGTTAC 59.824 37.037 0.00 0.00 0.00 2.50
195 196 3.507162 TTCCATTCACACACTCCATGT 57.493 42.857 0.00 0.00 44.81 3.21
198 199 2.622942 GCTTTTCCATTCACACACTCCA 59.377 45.455 0.00 0.00 0.00 3.86
273 274 1.165270 AAGCATAGTTTGGGTCGCAC 58.835 50.000 0.00 0.00 0.00 5.34
293 294 9.678941 GACTCATCAATCGTCACTTTATATGTA 57.321 33.333 0.00 0.00 0.00 2.29
298 299 9.201127 CATATGACTCATCAATCGTCACTTTAT 57.799 33.333 0.00 0.00 40.11 1.40
307 308 4.151867 CACCTGCATATGACTCATCAATCG 59.848 45.833 6.97 0.00 38.69 3.34
336 337 8.915871 ATGATCATCAAATTTACTTTTCGGTG 57.084 30.769 1.18 0.00 0.00 4.94
337 338 8.190784 GGATGATCATCAAATTTACTTTTCGGT 58.809 33.333 31.49 0.00 39.54 4.69
348 349 9.863650 AGTCTAATCTTGGATGATCATCAAATT 57.136 29.630 31.49 24.30 39.54 1.82
429 430 7.542130 GGTACAAATTAGCTTTTCCATTCACAG 59.458 37.037 0.00 0.00 0.00 3.66
451 452 7.318141 TGTAAGCTTGTACATGAGTTAGGTAC 58.682 38.462 9.86 3.14 44.58 3.34
471 472 7.867752 TCTTTTTACGAAACCCATTCTGTAAG 58.132 34.615 0.00 0.00 37.80 2.34
489 490 7.865385 GCATAATTTGGGTCGCATATCTTTTTA 59.135 33.333 0.00 0.00 0.00 1.52
510 511 7.920160 TCATCACTTTACATGTCAAGCATAA 57.080 32.000 17.72 3.75 35.74 1.90
558 582 3.132160 TCGAATGTACTTTTCGGCACAA 58.868 40.909 22.52 8.05 44.55 3.33
577 601 5.207110 AGTCTAATCTTGGGTGATCATCG 57.793 43.478 0.00 0.00 0.00 3.84
586 610 2.749621 GCACCACAAGTCTAATCTTGGG 59.250 50.000 10.44 6.56 46.11 4.12
603 627 1.394618 TTGTTGTGTTAGGTGGCACC 58.605 50.000 29.32 29.32 38.99 5.01
1056 1081 5.798125 TGCTACAAATGGTTTCCAATTGA 57.202 34.783 19.29 6.23 44.56 2.57
1078 1103 1.678970 GGCATTGTCCGAAGCCCTT 60.679 57.895 0.00 0.00 41.25 3.95
1111 1136 3.834726 CAACTGTTGTTGCCCCGA 58.165 55.556 12.30 0.00 45.57 5.14
1197 1222 0.536006 GCTGCTCTCCCTGTGTTTGT 60.536 55.000 0.00 0.00 0.00 2.83
1233 1258 0.385029 GACAGCATTGGTGTTGCACA 59.615 50.000 21.36 0.00 44.55 4.57
1273 1298 2.498056 CCTTGCACCGGGTTTGCTT 61.498 57.895 15.67 0.00 40.86 3.91
1303 1328 3.718434 TGTTGAATGATAGCCTCCTCCAT 59.282 43.478 0.00 0.00 0.00 3.41
1308 1333 4.142381 GGTTGTTGTTGAATGATAGCCTCC 60.142 45.833 0.00 0.00 0.00 4.30
1349 1374 3.994853 GTGCTTGCTGTTGGGGCC 61.995 66.667 0.00 0.00 0.00 5.80
1558 1583 1.747709 CAGCTTGTAGGCTTCTGCAT 58.252 50.000 0.00 0.00 41.00 3.96
1572 1597 2.203195 TGCACGTTCTGGCAGCTT 60.203 55.556 10.34 0.00 34.58 3.74
1621 1646 1.746615 GGCAGCGGAATTGCTCTGA 60.747 57.895 19.64 0.00 45.23 3.27
1683 1708 1.762708 CTTCCTGTTGTGGTTGGTGT 58.237 50.000 0.00 0.00 0.00 4.16
1741 1787 4.277257 TGTAGATTTTGCACATCGATGC 57.723 40.909 25.11 14.70 46.32 3.91
1743 1789 4.516698 GGGATGTAGATTTTGCACATCGAT 59.483 41.667 0.00 0.00 46.15 3.59
1786 1832 1.427072 ATGCTATAGGGGGTGGTGGC 61.427 60.000 1.04 0.00 0.00 5.01
1823 1869 1.030457 CTAGCAGGTACCACCGGTAG 58.970 60.000 15.94 16.07 44.90 3.18
1860 1906 8.095937 TGATGCATGACATTTTTATTTTTGCA 57.904 26.923 2.46 0.00 39.84 4.08
1867 1913 8.201464 ACACATGATGATGCATGACATTTTTAT 58.799 29.630 2.46 0.00 46.64 1.40
1868 1914 7.489757 CACACATGATGATGCATGACATTTTTA 59.510 33.333 2.46 0.00 46.64 1.52
1869 1915 6.312672 CACACATGATGATGCATGACATTTTT 59.687 34.615 2.46 0.00 46.64 1.94
1895 1942 8.807948 ATTTCCATGTTGCAATTAGTACTAGT 57.192 30.769 0.59 0.00 0.00 2.57
1924 1971 4.828939 TGCTTCATTCAGGAACATCTGTTT 59.171 37.500 0.00 0.00 38.56 2.83
2100 2151 0.250770 AAAGCCGGACCCTTCTTGAC 60.251 55.000 5.05 0.00 0.00 3.18
2111 2162 3.641437 CTTTGTTGATTCAAAGCCGGA 57.359 42.857 5.05 0.00 44.57 5.14
2124 2175 2.624838 AGGCCAGTTGATGACTTTGTTG 59.375 45.455 5.01 0.00 36.10 3.33
2143 2194 5.220854 GGATGATGACCGTTGTAATTTCAGG 60.221 44.000 0.00 0.00 0.00 3.86
2250 2302 9.816787 TTTAAAGTTGGTGTTAGATAGGGAATT 57.183 29.630 0.00 0.00 0.00 2.17
2358 2418 6.406692 TCTGACTTAGTTGCTTCTAGTGTT 57.593 37.500 0.00 0.00 0.00 3.32
2359 2419 6.209589 TGATCTGACTTAGTTGCTTCTAGTGT 59.790 38.462 0.00 0.00 0.00 3.55
2371 2432 7.445121 TGACAATGAACTTGATCTGACTTAGT 58.555 34.615 0.00 0.00 38.29 2.24
2391 2452 0.893270 CCCGGTGAAGCCAATGACAA 60.893 55.000 0.00 0.00 36.97 3.18
2431 2492 3.240134 ATGTGCCGCTCGGTGTTCT 62.240 57.895 10.24 0.00 37.65 3.01
2449 2510 4.988716 AGACGACCACCCGCCTCA 62.989 66.667 0.00 0.00 0.00 3.86
2464 2525 1.480954 GGTTGGTATTCCAGAGCGAGA 59.519 52.381 0.00 0.00 45.22 4.04
2465 2526 1.802880 CGGTTGGTATTCCAGAGCGAG 60.803 57.143 14.96 0.00 45.22 5.03
2472 2533 2.158871 GCCTACATCGGTTGGTATTCCA 60.159 50.000 0.00 0.00 41.33 3.53
2511 2572 1.066215 ACCACAGCATATTCTCGTGCA 60.066 47.619 0.00 0.00 43.63 4.57
2519 2580 1.755179 GCAGTCCACCACAGCATATT 58.245 50.000 0.00 0.00 37.46 1.28
2528 2589 2.899838 GCACAACGCAGTCCACCA 60.900 61.111 0.00 0.00 45.00 4.17
2579 2646 0.538516 AGACTGAGGTCACAGCTCGT 60.539 55.000 0.00 0.33 45.17 4.18
2649 2734 0.694771 GCTGCTCCCATGATCCCATA 59.305 55.000 0.00 0.00 0.00 2.74
2684 2769 2.203788 AACTCCCAGACGCTCCCA 60.204 61.111 0.00 0.00 0.00 4.37
2694 2779 4.299796 GGGCTTGCCCAACTCCCA 62.300 66.667 24.50 0.00 36.96 4.37
2698 2783 4.204028 ACACGGGCTTGCCCAACT 62.204 61.111 27.80 8.84 34.21 3.16
2739 2827 1.202806 TGCATTTGAGGGGATCGATCC 60.203 52.381 32.57 32.57 46.41 3.36
2747 2835 4.183686 CGCGCTGCATTTGAGGGG 62.184 66.667 5.56 0.00 0.00 4.79
2764 2852 2.282820 GTGAGCTATCTTTGCAGTACGC 59.717 50.000 0.00 3.22 42.89 4.42
2777 2865 4.559300 GCCATTTGTGTGTTTGTGAGCTAT 60.559 41.667 0.00 0.00 0.00 2.97
2788 2876 2.503331 TCAATCGAGCCATTTGTGTGT 58.497 42.857 0.00 0.00 0.00 3.72
2796 2884 4.162040 AGAGGAAAATCAATCGAGCCAT 57.838 40.909 0.00 0.00 0.00 4.40
2797 2885 3.634397 AGAGGAAAATCAATCGAGCCA 57.366 42.857 0.00 0.00 0.00 4.75
2798 2886 4.876107 TGTTAGAGGAAAATCAATCGAGCC 59.124 41.667 0.00 0.00 0.00 4.70
2815 2903 2.610433 CATGCTCGTTCTGCTGTTAGA 58.390 47.619 0.00 0.00 0.00 2.10
2819 2907 2.385875 CGCATGCTCGTTCTGCTGT 61.386 57.895 17.13 0.00 33.75 4.40
2820 2908 2.398429 CGCATGCTCGTTCTGCTG 59.602 61.111 17.13 0.00 33.75 4.41
2821 2909 3.494336 GCGCATGCTCGTTCTGCT 61.494 61.111 17.13 0.00 38.39 4.24


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

AutoCloner maintained by Alex Coulton.