Multiple sequence alignment - TraesCS3D01G078700

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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 TraesCS3D01G078700 chr3D 100.000 4134 0 0 1 4134 39304027 39299894 0.000000e+00 7635.0
1 TraesCS3D01G078700 chr3D 86.205 1515 110 33 1811 3263 39208902 39207425 0.000000e+00 1548.0
2 TraesCS3D01G078700 chr3D 89.234 483 28 12 3262 3736 39207398 39206932 2.140000e-162 582.0
3 TraesCS3D01G078700 chr3D 89.306 346 24 5 3765 4100 39206935 39206593 4.940000e-114 422.0
4 TraesCS3D01G078700 chr3B 89.442 2652 144 35 610 3202 62217825 62215251 0.000000e+00 3221.0
5 TraesCS3D01G078700 chr3B 88.411 1510 115 27 1735 3203 62012012 62010522 0.000000e+00 1764.0
6 TraesCS3D01G078700 chr3B 94.886 880 34 9 3262 4133 62215129 62214253 0.000000e+00 1365.0
7 TraesCS3D01G078700 chr3B 89.447 796 45 15 3262 4039 62010341 62009567 0.000000e+00 968.0
8 TraesCS3D01G078700 chr3B 86.101 554 49 13 127 666 62218344 62217805 4.640000e-159 571.0
9 TraesCS3D01G078700 chr3B 88.722 133 13 1 4 136 62218498 62218368 1.190000e-35 161.0
10 TraesCS3D01G078700 chr3B 100.000 47 0 0 3217 3263 62010414 62010368 2.050000e-13 87.9
11 TraesCS3D01G078700 chr3A 89.069 2589 173 42 13 2509 50642133 50639563 0.000000e+00 3112.0
12 TraesCS3D01G078700 chr3A 91.682 1611 57 28 2556 4134 50639561 50637996 0.000000e+00 2161.0
13 TraesCS3D01G078700 chr3A 88.770 1024 74 19 1493 2493 50548184 50547179 0.000000e+00 1216.0
14 TraesCS3D01G078700 chr3A 88.966 725 37 11 2581 3266 50547138 50546418 0.000000e+00 856.0
15 TraesCS3D01G078700 chr3A 88.281 512 42 9 3262 3765 50546385 50545884 7.650000e-167 597.0
16 TraesCS3D01G078700 chr3A 89.597 298 25 6 3838 4134 50545785 50545493 1.400000e-99 374.0
17 TraesCS3D01G078700 chr7B 89.625 453 31 8 1541 1992 698630822 698630385 2.790000e-156 562.0
18 TraesCS3D01G078700 chr7B 90.023 441 28 8 1552 1991 684165019 684165444 1.300000e-154 556.0
19 TraesCS3D01G078700 chr6B 89.602 452 31 8 1542 1992 68221069 68221505 1.000000e-155 560.0
20 TraesCS3D01G078700 chr5B 88.938 452 34 6 1542 1992 385249834 385250270 1.010000e-150 544.0
21 TraesCS3D01G078700 chr5B 86.161 448 46 8 1769 2209 598669446 598669884 1.740000e-128 470.0
22 TraesCS3D01G078700 chr5A 88.274 452 37 10 1542 1992 564680197 564679761 1.020000e-145 527.0
23 TraesCS3D01G078700 chr5A 85.156 384 45 8 1769 2148 632224342 632223967 2.330000e-102 383.0
24 TraesCS3D01G078700 chr4A 87.305 449 41 8 1545 1992 661807955 661807522 2.220000e-137 499.0
25 TraesCS3D01G078700 chr4A 83.251 203 34 0 2867 3069 173932155 173931953 1.960000e-43 187.0
26 TraesCS3D01G078700 chr2B 80.882 204 37 2 2866 3068 84817752 84817954 4.280000e-35 159.0
27 TraesCS3D01G078700 chr2A 80.882 204 37 2 2866 3068 54817556 54817354 4.280000e-35 159.0


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 TraesCS3D01G078700 chr3D 39299894 39304027 4133 True 7635.000000 7635 100.000000 1 4134 1 chr3D.!!$R1 4133
1 TraesCS3D01G078700 chr3D 39206593 39208902 2309 True 850.666667 1548 88.248333 1811 4100 3 chr3D.!!$R2 2289
2 TraesCS3D01G078700 chr3B 62214253 62218498 4245 True 1329.500000 3221 89.787750 4 4133 4 chr3B.!!$R2 4129
3 TraesCS3D01G078700 chr3B 62009567 62012012 2445 True 939.966667 1764 92.619333 1735 4039 3 chr3B.!!$R1 2304
4 TraesCS3D01G078700 chr3A 50637996 50642133 4137 True 2636.500000 3112 90.375500 13 4134 2 chr3A.!!$R2 4121
5 TraesCS3D01G078700 chr3A 50545493 50548184 2691 True 760.750000 1216 88.903500 1493 4134 4 chr3A.!!$R1 2641

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
957 1080 0.031010 AGATCCACCTCCACTACCCC 60.031 60.0 0.0 0.0 0.00 4.95 F
1757 1906 0.467384 ACTTGCCATCGGGATCTGAG 59.533 55.0 0.0 0.0 35.59 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 2999 0.917533 AGGGTTGAGCATGATGAGCT 59.082 50.0 0.0 0.0 46.82 4.09 R
3632 4055 0.037975 TGGGTTTTCGCCGTAGAGAC 60.038 55.0 0.0 0.0 0.00 3.36 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
34 35 5.710984 GTGGAACAATCGAGTCTTCTCTTA 58.289 41.667 1.08 0.00 44.16 2.10
57 58 0.605319 GTTGGTTCTCGACATGGCCA 60.605 55.000 8.56 8.56 0.00 5.36
64 65 3.499737 CGACATGGCCAGAACCGC 61.500 66.667 13.05 0.00 0.00 5.68
69 70 0.451783 CATGGCCAGAACCGCTAAAC 59.548 55.000 13.05 0.00 0.00 2.01
73 74 0.796927 GCCAGAACCGCTAAACTGAC 59.203 55.000 0.00 0.00 32.90 3.51
78 79 2.105993 AGAACCGCTAAACTGACCCTTT 59.894 45.455 0.00 0.00 0.00 3.11
219 254 3.157881 CCTCCCATATCTCGCTGAACTA 58.842 50.000 0.00 0.00 0.00 2.24
245 280 2.586792 GGCAACTCCGAGCTCCAT 59.413 61.111 8.47 0.00 0.00 3.41
261 296 3.680490 CTCCATATCCGAGCAGAGAGTA 58.320 50.000 0.00 0.00 0.00 2.59
309 344 0.253044 GGTATGCAGAGTTGAGGCCA 59.747 55.000 5.01 0.00 0.00 5.36
338 373 2.752807 GGATTAGGGAAGGGCGGCA 61.753 63.158 12.47 0.00 0.00 5.69
339 374 1.226262 GATTAGGGAAGGGCGGCAA 59.774 57.895 12.47 0.00 0.00 4.52
376 411 4.203618 GCGGAGGCAAAGAGGTAC 57.796 61.111 0.00 0.00 39.62 3.34
379 418 0.895530 CGGAGGCAAAGAGGTACAGA 59.104 55.000 0.00 0.00 0.00 3.41
385 424 1.009829 CAAAGAGGTACAGATGGCGC 58.990 55.000 0.00 0.00 0.00 6.53
414 454 6.038356 AGAGCAAACATTTTGAAAGTGTCTG 58.962 36.000 6.53 4.63 0.00 3.51
510 561 7.438757 CCAATGTCACACAAGAAAATCAAATCA 59.561 33.333 0.00 0.00 0.00 2.57
519 570 5.204409 AGAAAATCAAATCACAGCTGCAA 57.796 34.783 15.27 1.62 0.00 4.08
566 617 2.872245 GCCATAGCGTACACATCACATT 59.128 45.455 0.00 0.00 0.00 2.71
580 631 6.757947 ACACATCACATTGAAACCTTTTTCTG 59.242 34.615 0.00 0.00 41.64 3.02
582 633 4.692228 TCACATTGAAACCTTTTTCTGCC 58.308 39.130 0.00 0.00 41.64 4.85
583 634 4.405358 TCACATTGAAACCTTTTTCTGCCT 59.595 37.500 0.00 0.00 41.64 4.75
586 637 5.129320 ACATTGAAACCTTTTTCTGCCTCTT 59.871 36.000 0.00 0.00 41.64 2.85
587 638 4.918810 TGAAACCTTTTTCTGCCTCTTC 57.081 40.909 0.00 0.00 41.64 2.87
588 639 3.636764 TGAAACCTTTTTCTGCCTCTTCC 59.363 43.478 0.00 0.00 41.64 3.46
628 679 6.403866 AGCAATAATTGAGTGTTTGGTTGA 57.596 33.333 0.00 0.00 0.00 3.18
679 762 3.238441 GGTTCGATACGATCTGATCTGC 58.762 50.000 15.16 1.94 35.23 4.26
680 763 3.304726 GGTTCGATACGATCTGATCTGCA 60.305 47.826 15.16 1.31 35.23 4.41
681 764 4.480541 GTTCGATACGATCTGATCTGCAT 58.519 43.478 15.16 5.80 35.23 3.96
682 765 4.348198 TCGATACGATCTGATCTGCATC 57.652 45.455 15.16 12.41 0.00 3.91
683 766 4.006319 TCGATACGATCTGATCTGCATCT 58.994 43.478 15.16 0.00 0.00 2.90
685 768 4.142730 CGATACGATCTGATCTGCATCTGA 60.143 45.833 15.16 0.11 40.25 3.27
686 769 5.448904 CGATACGATCTGATCTGCATCTGAT 60.449 44.000 15.16 8.85 45.61 2.90
741 845 1.478137 GATCCGCGACATGTGTAGTC 58.522 55.000 8.23 0.00 0.00 2.59
854 977 4.046998 GTCGTGTGAGTGCGTGCG 62.047 66.667 0.00 0.00 0.00 5.34
957 1080 0.031010 AGATCCACCTCCACTACCCC 60.031 60.000 0.00 0.00 0.00 4.95
958 1081 1.382695 ATCCACCTCCACTACCCCG 60.383 63.158 0.00 0.00 0.00 5.73
959 1082 3.782443 CCACCTCCACTACCCCGC 61.782 72.222 0.00 0.00 0.00 6.13
960 1083 4.143333 CACCTCCACTACCCCGCG 62.143 72.222 0.00 0.00 0.00 6.46
1005 1132 1.340405 ACAGGCCAGTCAATCATGGAC 60.340 52.381 5.01 0.00 45.77 4.02
1320 1447 4.233635 CGCGAGGACGACTACGGG 62.234 72.222 0.00 0.00 44.46 5.28
1658 1803 2.253154 CGACGACACGCAGGTACA 59.747 61.111 0.00 0.00 0.00 2.90
1667 1813 2.224090 ACACGCAGGTACACACACATAA 60.224 45.455 0.00 0.00 0.00 1.90
1687 1833 1.202348 ACACCTCTGCAAGATCGATCG 60.202 52.381 19.33 9.36 45.62 3.69
1700 1846 1.065764 CGATCGAAGATCGGCCACA 59.934 57.895 20.74 0.00 45.12 4.17
1701 1847 1.209275 CGATCGAAGATCGGCCACAC 61.209 60.000 20.74 0.00 45.12 3.82
1757 1906 0.467384 ACTTGCCATCGGGATCTGAG 59.533 55.000 0.00 0.00 35.59 3.35
1765 1914 1.938585 TCGGGATCTGAGAACTTGGT 58.061 50.000 0.00 0.00 0.00 3.67
2007 2159 2.359230 GCGCTCAAGCACTCCCTT 60.359 61.111 0.00 0.00 42.21 3.95
2030 2182 2.421529 GCCAATCCCACCCTGTAACTAG 60.422 54.545 0.00 0.00 0.00 2.57
2036 2188 0.831307 CACCCTGTAACTAGCCTCCC 59.169 60.000 0.00 0.00 0.00 4.30
2123 2295 9.603921 ATCTTACATGATTTTGGCAAATTTAGG 57.396 29.630 14.29 11.08 32.35 2.69
2346 2549 6.459066 TGATATAAACTAGTCCAGCATGAGC 58.541 40.000 0.00 0.00 39.69 4.26
2392 2596 9.408069 GGAATTATATTTGTCTACTAGGTGTCG 57.592 37.037 0.00 0.00 0.00 4.35
2410 2614 4.731480 GTGTCGTATTCAGCAAACGTTTTT 59.269 37.500 11.66 0.00 37.83 1.94
2442 2646 6.972328 GTCAGTGTCAAAAACTTAAATCTGCA 59.028 34.615 0.00 0.00 0.00 4.41
2445 2649 7.275341 CAGTGTCAAAAACTTAAATCTGCAACA 59.725 33.333 0.00 0.00 0.00 3.33
2451 2655 7.755582 AAAACTTAAATCTGCAACAGTGTTC 57.244 32.000 5.27 2.17 32.61 3.18
2454 2658 5.536161 ACTTAAATCTGCAACAGTGTTCCAT 59.464 36.000 5.27 0.00 32.61 3.41
2468 2673 7.577303 ACAGTGTTCCATATTACCATCAAGAT 58.423 34.615 0.00 0.00 0.00 2.40
2473 2678 9.948964 TGTTCCATATTACCATCAAGATCATAG 57.051 33.333 0.00 0.00 0.00 2.23
2498 2703 8.131100 AGCTATAAAAATACTTCTACGCACGTA 58.869 33.333 2.56 2.56 0.00 3.57
2504 2709 3.293311 ACTTCTACGCACGTACATGTT 57.707 42.857 2.30 0.00 0.00 2.71
2506 2711 2.993449 TCTACGCACGTACATGTTCA 57.007 45.000 2.30 0.00 0.00 3.18
2515 2720 2.800544 ACGTACATGTTCACTGTCTTGC 59.199 45.455 2.30 0.00 0.00 4.01
2537 2742 7.840342 TGCTCAGCAAATTTTGTAAGAAAAA 57.160 28.000 0.00 0.00 34.76 1.94
2578 2818 3.599343 TGTGACTGTGATCTGTTATGGC 58.401 45.455 0.00 0.00 0.00 4.40
2579 2819 2.939103 GTGACTGTGATCTGTTATGGCC 59.061 50.000 0.00 0.00 0.00 5.36
2605 2845 2.626266 CCACATTAGCATCCATGTGCAT 59.374 45.455 10.57 0.00 46.10 3.96
2610 2850 7.147966 CCACATTAGCATCCATGTGCATATATT 60.148 37.037 10.57 0.00 46.10 1.28
2617 2857 5.694231 TCCATGTGCATATATTTCACAGC 57.306 39.130 17.54 4.28 42.98 4.40
2649 2892 1.276138 TGTCCATGAGCACTGTAGTGG 59.724 52.381 13.41 0.00 45.72 4.00
2654 2897 1.550327 TGAGCACTGTAGTGGAGAGG 58.450 55.000 13.41 0.00 45.72 3.69
2655 2898 1.075536 TGAGCACTGTAGTGGAGAGGA 59.924 52.381 13.41 0.00 45.72 3.71
2656 2899 1.748493 GAGCACTGTAGTGGAGAGGAG 59.252 57.143 13.41 0.00 45.72 3.69
2739 2983 9.903682 CAGAATAATTTGGTAATTGCTATGAGG 57.096 33.333 0.00 0.00 35.61 3.86
2755 2999 1.977129 TGAGGTGTCACATGGTCATGA 59.023 47.619 16.77 0.00 41.20 3.07
2758 3002 1.339438 GGTGTCACATGGTCATGAGCT 60.339 52.381 24.30 8.53 41.20 4.09
2759 3003 2.005451 GTGTCACATGGTCATGAGCTC 58.995 52.381 24.30 6.82 41.20 4.09
2760 3004 1.624813 TGTCACATGGTCATGAGCTCA 59.375 47.619 20.79 20.79 41.20 4.26
2956 3202 7.640240 GTGAACAACATCTACTTGAACTTTGAC 59.360 37.037 0.00 0.00 0.00 3.18
3133 3404 9.607988 TCAGTTTCACTAGAACAGTTTGATTAA 57.392 29.630 0.00 0.00 34.26 1.40
3459 3868 3.192212 TGCTGTGTGACATGTTTGTGAAA 59.808 39.130 0.00 0.00 35.79 2.69
3670 4093 2.416547 CCAAGCATTTCGACCAGTACAG 59.583 50.000 0.00 0.00 0.00 2.74
3769 4205 3.585862 TGAAAATCGACAGGAGCTGTAC 58.414 45.455 0.00 0.00 45.44 2.90
3817 4267 8.822652 AAAAATGGTTTTGCATTTGTTTTGAA 57.177 23.077 0.00 0.00 35.58 2.69
3820 4270 8.999220 AATGGTTTTGCATTTGTTTTGAATTT 57.001 23.077 0.00 0.00 0.00 1.82
3821 4271 7.807687 TGGTTTTGCATTTGTTTTGAATTTG 57.192 28.000 0.00 0.00 0.00 2.32
3901 4351 4.533707 ACTTTGATCTTGTCTGGGATCAGA 59.466 41.667 0.00 0.00 45.67 3.27
4052 4515 6.594788 TTTCTCATTCCAGCTTTAGCAATT 57.405 33.333 4.33 0.00 45.16 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.432252 CGATTGTTCCACACTAGTCAACC 59.568 47.826 0.00 0.00 0.00 3.77
2 3 4.038763 ACTCGATTGTTCCACACTAGTCAA 59.961 41.667 0.00 0.00 0.00 3.18
3 4 3.572682 ACTCGATTGTTCCACACTAGTCA 59.427 43.478 0.00 0.00 0.00 3.41
4 5 4.082679 AGACTCGATTGTTCCACACTAGTC 60.083 45.833 0.00 0.00 0.00 2.59
6 7 4.442375 AGACTCGATTGTTCCACACTAG 57.558 45.455 0.00 0.00 0.00 2.57
8 9 3.322254 AGAAGACTCGATTGTTCCACACT 59.678 43.478 8.75 0.00 0.00 3.55
9 10 3.654414 AGAAGACTCGATTGTTCCACAC 58.346 45.455 8.75 0.00 0.00 3.82
10 11 3.574396 AGAGAAGACTCGATTGTTCCACA 59.426 43.478 8.75 0.00 46.64 4.17
11 12 4.181309 AGAGAAGACTCGATTGTTCCAC 57.819 45.455 8.75 4.71 46.64 4.02
27 28 3.817084 TCGAGAACCAACGAGTAAGAGAA 59.183 43.478 0.00 0.00 34.49 2.87
34 35 1.336887 CCATGTCGAGAACCAACGAGT 60.337 52.381 0.00 0.00 39.16 4.18
57 58 1.349067 AGGGTCAGTTTAGCGGTTCT 58.651 50.000 0.00 0.00 0.00 3.01
64 65 4.757149 CAGAGTTGGAAAGGGTCAGTTTAG 59.243 45.833 0.00 0.00 0.00 1.85
69 70 2.938956 ACAGAGTTGGAAAGGGTCAG 57.061 50.000 0.00 0.00 0.00 3.51
73 74 1.340114 GGGCTACAGAGTTGGAAAGGG 60.340 57.143 0.00 0.00 0.00 3.95
78 79 1.605058 GAGCGGGCTACAGAGTTGGA 61.605 60.000 0.00 0.00 0.00 3.53
219 254 2.895424 CGGAGTTGCCTTGGGACCT 61.895 63.158 0.00 0.00 0.00 3.85
241 276 2.666272 ACTCTCTGCTCGGATATGGA 57.334 50.000 0.00 0.00 0.00 3.41
245 280 3.328050 TCATCCTACTCTCTGCTCGGATA 59.672 47.826 0.00 0.00 30.56 2.59
283 318 0.543749 AACTCTGCATACCTGAGGGC 59.456 55.000 2.38 0.00 42.10 5.19
290 325 0.253044 TGGCCTCAACTCTGCATACC 59.747 55.000 3.32 0.00 0.00 2.73
309 344 1.833049 CCTAATCCTCGGCGACCCT 60.833 63.158 4.99 0.00 0.00 4.34
338 373 1.192146 TCCACCTAGCCTCGCAACTT 61.192 55.000 0.00 0.00 0.00 2.66
339 374 1.608717 CTCCACCTAGCCTCGCAACT 61.609 60.000 0.00 0.00 0.00 3.16
348 383 3.541713 CCTCCGCCTCCACCTAGC 61.542 72.222 0.00 0.00 0.00 3.42
368 403 1.522569 GGCGCCATCTGTACCTCTT 59.477 57.895 24.80 0.00 0.00 2.85
371 406 4.530857 GCGGCGCCATCTGTACCT 62.531 66.667 28.98 0.00 0.00 3.08
374 409 4.569023 CTCGCGGCGCCATCTGTA 62.569 66.667 28.98 3.88 0.00 2.74
385 424 1.069296 TCAAAATGTTTGCTCTCGCGG 60.069 47.619 6.13 0.00 39.65 6.46
414 454 2.893637 AGCCACATGTGAACGACTATC 58.106 47.619 27.46 4.55 0.00 2.08
510 561 2.828095 TGCGGTTGTTGCAGCTGT 60.828 55.556 16.64 0.00 37.44 4.40
519 570 2.489938 AACATGGATAGTGCGGTTGT 57.510 45.000 0.00 0.00 0.00 3.32
566 617 3.636764 GGAAGAGGCAGAAAAAGGTTTCA 59.363 43.478 2.35 0.00 44.82 2.69
580 631 5.474876 TGAATTTCAAGAAAGAGGAAGAGGC 59.525 40.000 0.00 0.00 33.32 4.70
628 679 5.594317 AGTCAAGTACCAGCTCAACAAAAAT 59.406 36.000 0.00 0.00 0.00 1.82
679 762 4.704057 TGATCGTATCTCCTCCATCAGATG 59.296 45.833 3.04 3.04 31.57 2.90
680 763 4.928263 TGATCGTATCTCCTCCATCAGAT 58.072 43.478 0.00 0.00 33.75 2.90
681 764 4.373156 TGATCGTATCTCCTCCATCAGA 57.627 45.455 0.00 0.00 0.00 3.27
682 765 4.704057 TCATGATCGTATCTCCTCCATCAG 59.296 45.833 0.00 0.00 0.00 2.90
683 766 4.666512 TCATGATCGTATCTCCTCCATCA 58.333 43.478 0.00 0.00 0.00 3.07
685 768 6.617782 AAATCATGATCGTATCTCCTCCAT 57.382 37.500 9.06 0.00 0.00 3.41
686 769 6.041979 TGAAAATCATGATCGTATCTCCTCCA 59.958 38.462 9.06 0.00 0.00 3.86
732 836 2.812591 ACTTCACTCGTCGACTACACAT 59.187 45.455 14.70 0.00 0.00 3.21
741 845 2.177977 GCATACAGACTTCACTCGTCG 58.822 52.381 0.00 0.00 36.53 5.12
745 849 2.159558 TCGACGCATACAGACTTCACTC 60.160 50.000 0.00 0.00 0.00 3.51
958 1081 4.829518 GGAAATGGGAACGCGCGC 62.830 66.667 32.58 23.91 0.00 6.86
959 1082 4.174129 GGGAAATGGGAACGCGCG 62.174 66.667 30.96 30.96 0.00 6.86
960 1083 4.174129 CGGGAAATGGGAACGCGC 62.174 66.667 5.73 0.00 33.89 6.86
1658 1803 2.928801 TGCAGAGGTGTTATGTGTGT 57.071 45.000 0.00 0.00 0.00 3.72
1667 1813 1.202348 CGATCGATCTTGCAGAGGTGT 60.202 52.381 22.43 0.00 0.00 4.16
1687 1833 0.745845 AGCATGTGTGGCCGATCTTC 60.746 55.000 0.00 0.00 0.00 2.87
1700 1846 0.839277 TCGGGATCATGGAAGCATGT 59.161 50.000 0.00 0.00 34.39 3.21
1701 1847 2.082231 GATCGGGATCATGGAAGCATG 58.918 52.381 3.84 0.00 37.74 4.06
1757 1906 2.427095 ACAAGGCAGAAACACCAAGTTC 59.573 45.455 0.00 0.00 40.26 3.01
1765 1914 3.631250 AGAAAAGGACAAGGCAGAAACA 58.369 40.909 0.00 0.00 0.00 2.83
2007 2159 1.143329 TTACAGGGTGGGATTGGCCA 61.143 55.000 0.00 0.00 38.95 5.36
2030 2182 2.124778 GAGCTGAAGCAGGGAGGC 60.125 66.667 4.90 0.00 45.16 4.70
2036 2188 1.134189 TGGATGGATGAGCTGAAGCAG 60.134 52.381 4.90 0.00 45.16 4.24
2094 2266 8.712285 AATTTGCCAAAATCATGTAAGATCTG 57.288 30.769 0.00 0.00 34.84 2.90
2123 2295 3.873361 TGCTTGCAGATACTCTGTTATGC 59.127 43.478 6.06 9.15 45.94 3.14
2315 2518 9.273016 TGCTGGACTAGTTTATATCATTTTAGC 57.727 33.333 0.00 0.00 0.00 3.09
2379 2583 4.520179 TGCTGAATACGACACCTAGTAGA 58.480 43.478 0.00 0.00 0.00 2.59
2383 2587 3.303495 CGTTTGCTGAATACGACACCTAG 59.697 47.826 0.00 0.00 37.47 3.02
2392 2596 9.909043 ACAAAATTAAAAACGTTTGCTGAATAC 57.091 25.926 15.46 0.00 34.94 1.89
2394 2598 8.660373 TGACAAAATTAAAAACGTTTGCTGAAT 58.340 25.926 15.46 8.89 34.94 2.57
2473 2678 7.158243 ACGTGCGTAGAAGTATTTTTATAGC 57.842 36.000 0.00 0.00 0.00 2.97
2489 2694 2.287728 ACAGTGAACATGTACGTGCGTA 60.288 45.455 15.12 0.00 0.00 4.42
2493 2698 3.362986 GCAAGACAGTGAACATGTACGTG 60.363 47.826 13.64 13.64 0.00 4.49
2494 2699 2.800544 GCAAGACAGTGAACATGTACGT 59.199 45.455 0.00 0.00 0.00 3.57
2495 2700 3.059884 AGCAAGACAGTGAACATGTACG 58.940 45.455 0.00 0.00 0.00 3.67
2498 2703 3.136763 CTGAGCAAGACAGTGAACATGT 58.863 45.455 0.00 0.00 0.00 3.21
2537 2742 4.036734 CACAGCTGGTACACTTGACATTTT 59.963 41.667 19.93 0.00 0.00 1.82
2538 2743 3.565482 CACAGCTGGTACACTTGACATTT 59.435 43.478 19.93 0.00 0.00 2.32
2539 2744 3.141398 CACAGCTGGTACACTTGACATT 58.859 45.455 19.93 0.00 0.00 2.71
2540 2745 2.368548 TCACAGCTGGTACACTTGACAT 59.631 45.455 19.93 0.00 0.00 3.06
2541 2746 1.760029 TCACAGCTGGTACACTTGACA 59.240 47.619 19.93 0.00 0.00 3.58
2542 2747 2.135933 GTCACAGCTGGTACACTTGAC 58.864 52.381 19.93 16.16 0.00 3.18
2544 2749 2.138320 CAGTCACAGCTGGTACACTTG 58.862 52.381 19.93 5.22 33.11 3.16
2545 2750 1.762957 ACAGTCACAGCTGGTACACTT 59.237 47.619 19.93 1.29 40.59 3.16
2547 2752 1.068588 TCACAGTCACAGCTGGTACAC 59.931 52.381 19.93 8.49 40.59 2.90
2554 2794 4.502016 CATAACAGATCACAGTCACAGCT 58.498 43.478 0.00 0.00 0.00 4.24
2578 2818 1.215173 TGGATGCTAATGTGGAAGGGG 59.785 52.381 0.00 0.00 0.00 4.79
2579 2819 2.734755 TGGATGCTAATGTGGAAGGG 57.265 50.000 0.00 0.00 0.00 3.95
2605 2845 6.216801 ACCGTAGAAGTGCTGTGAAATATA 57.783 37.500 0.00 0.00 0.00 0.86
2610 2850 2.159014 ACAACCGTAGAAGTGCTGTGAA 60.159 45.455 0.00 0.00 0.00 3.18
2617 2857 3.254060 CTCATGGACAACCGTAGAAGTG 58.746 50.000 0.00 0.00 39.42 3.16
2619 2859 2.271800 GCTCATGGACAACCGTAGAAG 58.728 52.381 0.00 0.00 39.42 2.85
2656 2899 8.833231 TCACCATATTATTTTAGAGCTAGTGC 57.167 34.615 0.00 0.00 40.05 4.40
2739 2983 2.005451 GAGCTCATGACCATGTGACAC 58.995 52.381 9.40 0.00 39.72 3.67
2755 2999 0.917533 AGGGTTGAGCATGATGAGCT 59.082 50.000 0.00 0.00 46.82 4.09
2758 3002 2.306805 ACTTCAGGGTTGAGCATGATGA 59.693 45.455 14.69 0.00 34.15 2.92
2759 3003 2.422479 CACTTCAGGGTTGAGCATGATG 59.578 50.000 0.00 8.53 34.15 3.07
2760 3004 2.719739 CACTTCAGGGTTGAGCATGAT 58.280 47.619 0.00 0.00 34.15 2.45
3133 3404 6.761312 TGAGAAGAAACAAATGGCAATTGAT 58.239 32.000 21.42 7.28 0.00 2.57
3632 4055 0.037975 TGGGTTTTCGCCGTAGAGAC 60.038 55.000 0.00 0.00 0.00 3.36
3670 4093 7.168135 CCAGAAAATAAGCACAGAACTTGTTTC 59.832 37.037 0.00 0.00 37.44 2.78
3716 4139 4.018050 AGGAACAATTATGCTTCCTCAGGT 60.018 41.667 0.00 0.00 40.21 4.00
3784 4221 9.018716 CAAATGCAAAACCATTTTTAAAAGGAC 57.981 29.630 11.99 0.00 41.97 3.85
3850 4300 4.320788 GCACCTCAAAGATCTCACCAAAAG 60.321 45.833 0.00 0.00 0.00 2.27
4052 4515 5.190726 TGGACAGGACATGATACCAACAATA 59.809 40.000 0.00 0.00 31.43 1.90


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

AutoCloner maintained by Alex Coulton.