Multiple sequence alignment - TraesCS3D01G073800

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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 TraesCS3D01G073800 chr3D 100.000 3267 0 0 1 3267 33712475 33715741 0.000000e+00 6034
1 TraesCS3D01G073800 chr3D 89.431 2583 249 11 706 3267 335958357 335955778 0.000000e+00 3236
2 TraesCS3D01G073800 chr3D 86.106 547 57 6 2740 3267 483310068 483309522 3.660000e-159 571
3 TraesCS3D01G073800 chr3D 89.919 248 25 0 3020 3267 582389543 582389790 1.460000e-83 320
4 TraesCS3D01G073800 chr4D 91.096 3302 237 13 2 3267 326946540 326943260 0.000000e+00 4416
5 TraesCS3D01G073800 chr5D 90.532 3306 267 23 2 3267 318511296 318514595 0.000000e+00 4329
6 TraesCS3D01G073800 chr5D 91.059 2852 227 14 2 2835 534901574 534904415 0.000000e+00 3829
7 TraesCS3D01G073800 chr2D 90.051 3307 283 26 2 3267 102508836 102505535 0.000000e+00 4242
8 TraesCS3D01G073800 chr2D 89.561 3305 299 24 2 3267 41763764 41760467 0.000000e+00 4150
9 TraesCS3D01G073800 chr2D 89.241 3309 309 23 2 3267 38982227 38978923 0.000000e+00 4095
10 TraesCS3D01G073800 chr2D 88.966 2583 262 10 706 3267 536060740 536058160 0.000000e+00 3169
11 TraesCS3D01G073800 chr7D 90.422 3247 262 30 2 3208 182871956 182875193 0.000000e+00 4228
12 TraesCS3D01G073800 chr7D 89.937 3309 283 29 2 3267 147042061 147045362 0.000000e+00 4220
13 TraesCS3D01G073800 chr1D 88.735 3311 323 25 2 3267 32397131 32393826 0.000000e+00 4002
14 TraesCS3D01G073800 chr1D 89.078 2234 221 10 1054 3267 472638617 472640847 0.000000e+00 2752
15 TraesCS3D01G073800 chr1D 90.421 1973 146 11 1319 3267 71595540 71593587 0.000000e+00 2556
16 TraesCS3D01G073800 chr1D 86.289 547 56 6 2740 3267 100540224 100540770 7.860000e-161 577
17 TraesCS3D01G073800 chrUn 90.585 2921 244 20 2 2898 91267079 91269992 0.000000e+00 3842
18 TraesCS3D01G073800 chr4B 88.720 3032 292 26 129 3115 57702783 57699757 0.000000e+00 3659
19 TraesCS3D01G073800 chr6D 89.449 2379 228 10 909 3267 429256142 429258517 0.000000e+00 2981
20 TraesCS3D01G073800 chr6D 89.520 563 40 8 2 545 417414935 417415497 0.000000e+00 695
21 TraesCS3D01G073800 chr6D 86.289 547 56 6 2740 3267 437007969 437008515 7.860000e-161 577
22 TraesCS3D01G073800 chr7A 87.019 1117 97 15 2013 3105 291596186 291595094 0.000000e+00 1216


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 TraesCS3D01G073800 chr3D 33712475 33715741 3266 False 6034 6034 100.000 1 3267 1 chr3D.!!$F1 3266
1 TraesCS3D01G073800 chr3D 335955778 335958357 2579 True 3236 3236 89.431 706 3267 1 chr3D.!!$R1 2561
2 TraesCS3D01G073800 chr3D 483309522 483310068 546 True 571 571 86.106 2740 3267 1 chr3D.!!$R2 527
3 TraesCS3D01G073800 chr4D 326943260 326946540 3280 True 4416 4416 91.096 2 3267 1 chr4D.!!$R1 3265
4 TraesCS3D01G073800 chr5D 318511296 318514595 3299 False 4329 4329 90.532 2 3267 1 chr5D.!!$F1 3265
5 TraesCS3D01G073800 chr5D 534901574 534904415 2841 False 3829 3829 91.059 2 2835 1 chr5D.!!$F2 2833
6 TraesCS3D01G073800 chr2D 102505535 102508836 3301 True 4242 4242 90.051 2 3267 1 chr2D.!!$R3 3265
7 TraesCS3D01G073800 chr2D 41760467 41763764 3297 True 4150 4150 89.561 2 3267 1 chr2D.!!$R2 3265
8 TraesCS3D01G073800 chr2D 38978923 38982227 3304 True 4095 4095 89.241 2 3267 1 chr2D.!!$R1 3265
9 TraesCS3D01G073800 chr2D 536058160 536060740 2580 True 3169 3169 88.966 706 3267 1 chr2D.!!$R4 2561
10 TraesCS3D01G073800 chr7D 182871956 182875193 3237 False 4228 4228 90.422 2 3208 1 chr7D.!!$F2 3206
11 TraesCS3D01G073800 chr7D 147042061 147045362 3301 False 4220 4220 89.937 2 3267 1 chr7D.!!$F1 3265
12 TraesCS3D01G073800 chr1D 32393826 32397131 3305 True 4002 4002 88.735 2 3267 1 chr1D.!!$R1 3265
13 TraesCS3D01G073800 chr1D 472638617 472640847 2230 False 2752 2752 89.078 1054 3267 1 chr1D.!!$F2 2213
14 TraesCS3D01G073800 chr1D 71593587 71595540 1953 True 2556 2556 90.421 1319 3267 1 chr1D.!!$R2 1948
15 TraesCS3D01G073800 chr1D 100540224 100540770 546 False 577 577 86.289 2740 3267 1 chr1D.!!$F1 527
16 TraesCS3D01G073800 chrUn 91267079 91269992 2913 False 3842 3842 90.585 2 2898 1 chrUn.!!$F1 2896
17 TraesCS3D01G073800 chr4B 57699757 57702783 3026 True 3659 3659 88.720 129 3115 1 chr4B.!!$R1 2986
18 TraesCS3D01G073800 chr6D 429256142 429258517 2375 False 2981 2981 89.449 909 3267 1 chr6D.!!$F2 2358
19 TraesCS3D01G073800 chr6D 417414935 417415497 562 False 695 695 89.520 2 545 1 chr6D.!!$F1 543
20 TraesCS3D01G073800 chr6D 437007969 437008515 546 False 577 577 86.289 2740 3267 1 chr6D.!!$F3 527
21 TraesCS3D01G073800 chr7A 291595094 291596186 1092 True 1216 1216 87.019 2013 3105 1 chr7A.!!$R1 1092

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
844 868 0.747255 CCTGACTACCATGACGAGGG 59.253 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2716 2752 0.251341 GGATGGTTGTGGTGCCTTCT 60.251 55.0 0.0 0.0 31.82 2.85 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
53 55 2.753452 GTGTGTATCTCGAAGTGGAGGA 59.247 50.000 0.00 0.00 34.74 3.71
90 92 1.135228 GTGGCGGTTGTTTTGTGAGTT 60.135 47.619 0.00 0.00 0.00 3.01
94 96 2.851824 GCGGTTGTTTTGTGAGTTGAAG 59.148 45.455 0.00 0.00 0.00 3.02
142 144 0.905337 AACGGAGGAGGAGACCTTGG 60.905 60.000 0.00 0.00 40.73 3.61
256 275 1.953559 TAGCATCAAGATTCGTGCCC 58.046 50.000 0.00 0.00 38.31 5.36
261 280 2.044946 AAGATTCGTGCCCCCTGC 60.045 61.111 0.00 0.00 41.77 4.85
351 372 5.129815 AGGCACTACCGTTGGAATTATAGAA 59.870 40.000 0.00 0.00 46.52 2.10
410 432 1.529948 CAGGGGCATGCATCCGAAT 60.530 57.895 21.36 1.99 0.00 3.34
589 611 0.796312 CAGCATTGGTCGTGTGGTAC 59.204 55.000 0.00 0.00 0.00 3.34
665 688 2.353889 GCTGAATGGAGTGCACACTATG 59.646 50.000 21.04 5.89 42.66 2.23
713 736 8.040132 TGCTTAAATGGCTTATATGCAAAAACT 58.960 29.630 12.22 0.00 34.04 2.66
739 763 1.785951 GTGCTTAACCGGACGCTTC 59.214 57.895 9.46 0.00 0.00 3.86
747 771 2.732094 CGGACGCTTCGACGGTTT 60.732 61.111 0.00 0.00 37.37 3.27
754 778 2.034076 CGCTTCGACGGTTTCTTTTTG 58.966 47.619 0.00 0.00 0.00 2.44
844 868 0.747255 CCTGACTACCATGACGAGGG 59.253 60.000 0.00 0.00 0.00 4.30
869 893 1.079127 CAACCGCTTCCTCCACGAT 60.079 57.895 0.00 0.00 0.00 3.73
879 903 2.542550 TCCTCCACGATCCAAACCTTA 58.457 47.619 0.00 0.00 0.00 2.69
969 993 5.265191 ACTAGCAACTCCTCACAATCTCTA 58.735 41.667 0.00 0.00 0.00 2.43
978 1002 5.523588 TCCTCACAATCTCTATCTCAAGGT 58.476 41.667 0.00 0.00 0.00 3.50
1050 1074 1.183030 ATGGTGAGACGTCCGACCAA 61.183 55.000 29.97 18.43 41.74 3.67
1068 1092 1.874345 AAAGCACCGAGGTCGACGAT 61.874 55.000 9.92 0.00 43.02 3.73
1193 1217 4.100035 TGAAGCCGACAAGATGATCAGTAT 59.900 41.667 0.09 0.00 0.00 2.12
1233 1257 1.614317 GGCTTGTACCCTCAGCACATT 60.614 52.381 5.98 0.00 0.00 2.71
1271 1296 1.421646 CACCAGGGAAGACAAACCTCT 59.578 52.381 0.00 0.00 30.66 3.69
1398 1423 9.661187 CTTCATGCTTCTGTTTAATTAGCTATG 57.339 33.333 0.00 0.00 33.15 2.23
1407 1432 1.986882 AATTAGCTATGGCACCCTGC 58.013 50.000 3.10 0.00 44.08 4.85
1451 1477 5.724328 TGGACTTGATGTATCAGTGAAGTC 58.276 41.667 12.67 12.67 38.93 3.01
1491 1517 7.624549 AGCAGAATAGATTTTGAACCTGACTA 58.375 34.615 0.00 0.00 0.00 2.59
1588 1614 6.914259 TGATGTTCTAGTGTAGTCTCTGTTG 58.086 40.000 0.00 0.00 0.00 3.33
1589 1615 6.715264 TGATGTTCTAGTGTAGTCTCTGTTGA 59.285 38.462 0.00 0.00 0.00 3.18
1598 1624 6.016943 AGTGTAGTCTCTGTTGAAGTGTAGTC 60.017 42.308 0.00 0.00 0.00 2.59
1647 1673 8.562892 AGTTCAGTTTCTTGAATTGATGTAGTG 58.437 33.333 0.00 0.00 39.13 2.74
1648 1674 8.345565 GTTCAGTTTCTTGAATTGATGTAGTGT 58.654 33.333 0.00 0.00 39.13 3.55
1649 1675 8.450578 TCAGTTTCTTGAATTGATGTAGTGTT 57.549 30.769 0.00 0.00 30.04 3.32
1654 1680 6.061441 TCTTGAATTGATGTAGTGTTGTGGT 58.939 36.000 0.00 0.00 0.00 4.16
1682 1708 7.288560 AGAAGCAGATAGGTCATTGATTCAAT 58.711 34.615 6.06 6.06 38.15 2.57
1740 1767 8.435430 GCTTGTATTTAATTTCTGAACTTTGCC 58.565 33.333 0.00 0.00 0.00 4.52
1785 1814 7.406799 TCATGCATGAATTGTACGTACTATG 57.593 36.000 26.87 19.54 33.08 2.23
1800 1829 5.747197 ACGTACTATGTAAGCATGTACTTGC 59.253 40.000 22.56 22.56 43.09 4.01
1889 1919 2.164624 CTGAAGGAGGACAGGTTCTACG 59.835 54.545 0.00 0.00 0.00 3.51
1967 1997 2.496470 GAGATCAACCCCGACAAGTACT 59.504 50.000 0.00 0.00 0.00 2.73
1994 2024 1.277842 TCCAGCGCAAATGGAGAGTTA 59.722 47.619 12.49 0.00 41.96 2.24
2001 2031 3.181530 CGCAAATGGAGAGTTACGTTCAG 60.182 47.826 0.00 0.00 0.00 3.02
2010 2040 3.006644 AGAGTTACGTTCAGGGGAAGAAC 59.993 47.826 0.00 0.00 41.41 3.01
2011 2041 2.701951 AGTTACGTTCAGGGGAAGAACA 59.298 45.455 0.00 0.00 44.22 3.18
2149 2181 5.292101 GCATAATTACCTCATCGAGTATGCC 59.708 44.000 10.28 0.00 35.50 4.40
2152 2184 1.109920 ACCTCATCGAGTATGCCGCT 61.110 55.000 0.00 0.00 35.38 5.52
2236 2268 3.080319 GAGTGCAAAAGAGGCAGAGAAT 58.920 45.455 0.00 0.00 42.85 2.40
2293 2325 6.137794 TGACGAAAACTTAGAAAATTGGCA 57.862 33.333 0.00 0.00 0.00 4.92
2312 2344 2.540931 GCATTGGAGTTGCTTGTGTTTG 59.459 45.455 0.00 0.00 37.14 2.93
2403 2436 8.015658 GTCATGTGTATCAGGTTAAACAAGTTC 58.984 37.037 0.00 0.00 0.00 3.01
2419 2452 4.213482 ACAAGTTCGCTTATGTCAGGTTTC 59.787 41.667 0.00 0.00 35.31 2.78
2420 2453 3.335579 AGTTCGCTTATGTCAGGTTTCC 58.664 45.455 0.00 0.00 0.00 3.13
2436 2469 5.977129 CAGGTTTCCAGTTTGTTTATGTGAC 59.023 40.000 0.00 0.00 0.00 3.67
2527 2561 7.715265 TGTTGCTCTTTACTCTAAGAACAAG 57.285 36.000 0.00 0.00 39.53 3.16
2552 2588 8.148999 AGAAAATAGAAAGTAGTCTTTGGACGT 58.851 33.333 0.00 0.00 46.29 4.34
2555 2591 4.377897 AGAAAGTAGTCTTTGGACGTTGG 58.622 43.478 0.00 0.00 46.29 3.77
2574 2610 3.472652 TGGGTACAGTTTAGTTGTGCAG 58.527 45.455 0.00 0.00 33.51 4.41
2605 2641 1.480137 CTTCTCGAGGAGTGGCAAGAT 59.520 52.381 13.02 0.00 0.00 2.40
2635 2671 4.208666 GGGTCGAAATACGCATTTAGAGAC 59.791 45.833 4.37 8.92 36.72 3.36
2664 2700 0.251787 TGCAGTCTCTAGAGCCACCA 60.252 55.000 15.35 6.86 0.00 4.17
2716 2752 4.632153 GGCAGTGAAGTCTCTACAGAAAA 58.368 43.478 0.00 0.00 0.00 2.29
2730 2767 2.427095 ACAGAAAAGAAGGCACCACAAC 59.573 45.455 0.00 0.00 0.00 3.32
2738 2779 1.978617 GGCACCACAACCATCCAGG 60.979 63.158 0.00 0.00 45.67 4.45
2752 2793 4.181010 CAGGGGCTCGTGGATGGG 62.181 72.222 0.00 0.00 0.00 4.00
2758 2799 2.808206 GCTCGTGGATGGGGTAGGG 61.808 68.421 0.00 0.00 0.00 3.53
2806 2847 1.385528 GGTCACGGTTTGGAAGTGTT 58.614 50.000 0.00 0.00 37.20 3.32
2836 2877 3.650647 GTGTGTGACACCATGGGAT 57.349 52.632 18.09 2.62 43.05 3.85
2900 2945 1.359459 GCAGGTACGTAAGGCACTGC 61.359 60.000 16.27 16.27 40.86 4.40
3000 3050 2.423577 GGTTAGAGATGCACGGTTGTT 58.576 47.619 0.00 0.00 0.00 2.83
3002 3052 4.189231 GGTTAGAGATGCACGGTTGTTAT 58.811 43.478 0.00 0.00 0.00 1.89
3010 3060 2.223595 TGCACGGTTGTTATGTTTGTGG 60.224 45.455 0.00 0.00 0.00 4.17
3017 3067 4.084013 GGTTGTTATGTTTGTGGAGAGACG 60.084 45.833 0.00 0.00 0.00 4.18
3024 3093 4.505808 TGTTTGTGGAGAGACGTTGTAAA 58.494 39.130 0.00 0.00 0.00 2.01
3026 3095 5.163834 TGTTTGTGGAGAGACGTTGTAAAAC 60.164 40.000 0.00 0.00 0.00 2.43
3029 3098 4.098960 TGTGGAGAGACGTTGTAAAACTCT 59.901 41.667 0.72 0.72 36.39 3.24
3046 3115 4.351938 TCGGGGCGTGAGACGTTG 62.352 66.667 0.00 0.00 44.73 4.10
3115 3184 1.395635 ACGGAAGTGGGGTTTTTGTC 58.604 50.000 0.00 0.00 46.97 3.18
3117 3186 0.671796 GGAAGTGGGGTTTTTGTCGG 59.328 55.000 0.00 0.00 0.00 4.79
3123 3192 1.281656 GGGTTTTTGTCGGTGCGAG 59.718 57.895 0.00 0.00 36.23 5.03
3171 3240 1.911357 AGTGTGATTCCAGAGGCATGA 59.089 47.619 0.00 0.00 0.00 3.07
3197 3266 3.428452 CGAATACGCAGTTAGGGAGTCAA 60.428 47.826 0.00 0.00 37.78 3.18
3249 3318 2.903855 GCATCACGGGCATGGAGG 60.904 66.667 0.00 0.00 0.00 4.30
3255 3324 4.047125 CGGGCATGGAGGGGTGTT 62.047 66.667 0.00 0.00 0.00 3.32
3258 3327 2.440599 GCATGGAGGGGTGTTGGT 59.559 61.111 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000717 GCGCCCAACAACACAAAGTAT 60.001 47.619 0.00 0.00 0.00 2.12
94 96 2.014857 GGGCCCAAATTCGAAGTAGAC 58.985 52.381 19.95 0.00 0.00 2.59
142 144 0.165944 CGAAACATTCCGCACTCACC 59.834 55.000 0.00 0.00 0.00 4.02
213 232 3.482722 TCAGACCGTCGAAGATTACAC 57.517 47.619 0.00 0.00 40.67 2.90
280 301 9.256477 CCTCACACGTTTATTAAGATGCTATAA 57.744 33.333 0.00 0.00 0.00 0.98
333 354 6.046593 CAGTGCTTCTATAATTCCAACGGTA 58.953 40.000 0.00 0.00 0.00 4.02
334 355 4.876107 CAGTGCTTCTATAATTCCAACGGT 59.124 41.667 0.00 0.00 0.00 4.83
335 356 4.273480 CCAGTGCTTCTATAATTCCAACGG 59.727 45.833 0.00 0.00 0.00 4.44
351 372 2.027745 CCACAGAGTTGATACCAGTGCT 60.028 50.000 0.00 0.00 0.00 4.40
410 432 3.679824 TCGTGACTCTCTGAGTGAGTA 57.320 47.619 16.22 0.00 43.53 2.59
430 452 6.403855 GCTCGTAACTCTAGAGACTTCACAAT 60.404 42.308 26.57 0.00 34.13 2.71
442 464 2.159037 TGACACACGCTCGTAACTCTAG 59.841 50.000 0.00 0.00 0.00 2.43
560 582 3.006967 ACGACCAATGCTGTAGAGACTTT 59.993 43.478 0.00 0.00 0.00 2.66
650 673 2.673893 CGCTTACATAGTGTGCACTCCA 60.674 50.000 19.41 3.58 42.54 3.86
703 726 8.696175 GTTAAGCACGTATAAAAGTTTTTGCAT 58.304 29.630 19.05 12.43 0.00 3.96
704 727 7.167801 GGTTAAGCACGTATAAAAGTTTTTGCA 59.832 33.333 19.05 0.00 0.00 4.08
713 736 3.611986 CGTCCGGTTAAGCACGTATAAAA 59.388 43.478 0.00 0.00 0.00 1.52
717 740 0.803380 GCGTCCGGTTAAGCACGTAT 60.803 55.000 15.93 0.00 34.69 3.06
739 763 0.659123 CCGGCAAAAAGAAACCGTCG 60.659 55.000 0.00 0.00 44.14 5.12
747 771 2.725008 CGGTTGCCGGCAAAAAGA 59.275 55.556 41.60 19.50 44.15 2.52
818 842 0.104304 CATGGTAGTCAGGGCGGTAC 59.896 60.000 0.00 0.00 0.00 3.34
828 852 1.065928 CGCCCTCGTCATGGTAGTC 59.934 63.158 0.00 0.00 0.00 2.59
858 882 1.358152 AGGTTTGGATCGTGGAGGAA 58.642 50.000 0.00 0.00 0.00 3.36
869 893 3.301274 CCCTTTTGTGGTAAGGTTTGGA 58.699 45.455 0.00 0.00 40.47 3.53
879 903 1.822615 GCAGTTGCCCTTTTGTGGT 59.177 52.632 0.00 0.00 34.31 4.16
902 926 2.533266 TCGGAATTGAGAGGCTATGC 57.467 50.000 0.00 0.00 0.00 3.14
910 934 4.558496 GCAATGGTGTTTTCGGAATTGAGA 60.558 41.667 0.00 0.00 0.00 3.27
969 993 1.227380 GCGATGGCGACCTTGAGAT 60.227 57.895 0.00 0.00 40.82 2.75
978 1002 3.531207 CTCCTCCAGCGATGGCGA 61.531 66.667 16.69 11.93 46.35 5.54
1050 1074 2.341101 ATCGTCGACCTCGGTGCTT 61.341 57.895 10.58 0.00 40.29 3.91
1068 1092 0.105194 TCTGACCAGGGACCTGAACA 60.105 55.000 19.65 15.96 46.30 3.18
1170 1194 2.234661 ACTGATCATCTTGTCGGCTTCA 59.765 45.455 0.00 0.00 0.00 3.02
1193 1217 1.330655 GCAGACCCTCTTCCGGATCA 61.331 60.000 4.15 0.00 0.00 2.92
1199 1223 2.960688 AAGCCGCAGACCCTCTTCC 61.961 63.158 0.00 0.00 0.00 3.46
1233 1257 0.599060 TGTACTCGACATCAACGCCA 59.401 50.000 0.00 0.00 31.20 5.69
1356 1381 4.943705 GCATGAAGAGGTTGGATTTGTAGA 59.056 41.667 0.00 0.00 0.00 2.59
1365 1390 2.787994 ACAGAAGCATGAAGAGGTTGG 58.212 47.619 0.00 0.00 0.00 3.77
1398 1423 3.608316 TTAATCAAATTGCAGGGTGCC 57.392 42.857 0.00 0.00 44.23 5.01
1429 1455 5.971763 AGACTTCACTGATACATCAAGTCC 58.028 41.667 14.08 2.80 39.78 3.85
1451 1477 8.389779 TCTATTCTGCTACATCTACTTCAGAG 57.610 38.462 0.00 0.00 36.48 3.35
1491 1517 9.369904 GCATCAAATACATAAACTGATTTGGTT 57.630 29.630 6.40 0.00 38.97 3.67
1581 1607 8.500753 AGTATAGAGACTACACTTCAACAGAG 57.499 38.462 0.00 0.00 0.00 3.35
1588 1614 9.724839 GAACATCAAGTATAGAGACTACACTTC 57.275 37.037 0.00 0.00 0.00 3.01
1589 1615 9.469097 AGAACATCAAGTATAGAGACTACACTT 57.531 33.333 0.00 0.00 0.00 3.16
1644 1670 4.150897 TCTGCTTCTTAACCACAACACT 57.849 40.909 0.00 0.00 0.00 3.55
1647 1673 5.246307 ACCTATCTGCTTCTTAACCACAAC 58.754 41.667 0.00 0.00 0.00 3.32
1648 1674 5.012664 TGACCTATCTGCTTCTTAACCACAA 59.987 40.000 0.00 0.00 0.00 3.33
1649 1675 4.530553 TGACCTATCTGCTTCTTAACCACA 59.469 41.667 0.00 0.00 0.00 4.17
1654 1680 8.267183 TGAATCAATGACCTATCTGCTTCTTAA 58.733 33.333 0.00 0.00 0.00 1.85
1765 1792 7.042992 TGCTTACATAGTACGTACAATTCATGC 60.043 37.037 26.55 20.58 0.00 4.06
1774 1801 7.096722 GCAAGTACATGCTTACATAGTACGTAC 60.097 40.741 18.10 18.10 43.06 3.67
1915 1945 2.028658 TCTTCGCAGCATCTCTTTGTCT 60.029 45.455 0.00 0.00 0.00 3.41
1967 1997 0.447406 CATTTGCGCTGGATGTCGAA 59.553 50.000 9.73 0.00 0.00 3.71
1994 2024 1.202770 CCTTGTTCTTCCCCTGAACGT 60.203 52.381 0.00 0.00 44.67 3.99
2001 2031 1.145119 AGTGGAACCTTGTTCTTCCCC 59.855 52.381 6.89 0.00 37.80 4.81
2127 2159 5.651530 CGGCATACTCGATGAGGTAATTAT 58.348 41.667 0.00 0.00 37.82 1.28
2128 2160 4.617530 GCGGCATACTCGATGAGGTAATTA 60.618 45.833 0.00 0.00 37.82 1.40
2152 2184 1.612676 AGGTGGCGTACGCATCTATA 58.387 50.000 37.99 15.92 44.11 1.31
2236 2268 5.124457 GCCGTAGTAGGGATCGTCATAATTA 59.876 44.000 13.15 0.00 0.00 1.40
2293 2325 3.784338 CACAAACACAAGCAACTCCAAT 58.216 40.909 0.00 0.00 0.00 3.16
2312 2344 6.072112 TGAAACAATAGAAAGGACAAGCAC 57.928 37.500 0.00 0.00 0.00 4.40
2350 2383 6.049263 AGAAACTGCTTCGTTCTAACAAAG 57.951 37.500 0.00 0.00 39.22 2.77
2352 2385 6.200286 CACTAGAAACTGCTTCGTTCTAACAA 59.800 38.462 0.00 0.00 39.22 2.83
2403 2436 2.699954 ACTGGAAACCTGACATAAGCG 58.300 47.619 0.00 0.00 0.00 4.68
2419 2452 6.130298 TGTTCAGTCACATAAACAAACTGG 57.870 37.500 0.00 0.00 38.27 4.00
2420 2453 7.250569 ACTTGTTCAGTCACATAAACAAACTG 58.749 34.615 0.00 0.00 40.10 3.16
2436 2469 8.507249 ACTTAGCAAGCTAAATAACTTGTTCAG 58.493 33.333 14.71 2.35 44.12 3.02
2475 2508 7.141363 ACTACTTCAAAATCACATGTTTGCTC 58.859 34.615 0.00 0.00 35.21 4.26
2527 2561 8.307921 ACGTCCAAAGACTACTTTCTATTTTC 57.692 34.615 0.00 0.00 43.41 2.29
2534 2568 3.497262 CCCAACGTCCAAAGACTACTTTC 59.503 47.826 0.00 0.00 43.41 2.62
2539 2574 2.964464 TGTACCCAACGTCCAAAGACTA 59.036 45.455 0.00 0.00 41.16 2.59
2552 2588 3.880490 CTGCACAACTAAACTGTACCCAA 59.120 43.478 0.00 0.00 0.00 4.12
2555 2591 4.124238 TGTCTGCACAACTAAACTGTACC 58.876 43.478 0.00 0.00 0.00 3.34
2605 2641 1.374560 CGTATTTCGACCCATGCCAA 58.625 50.000 0.00 0.00 42.86 4.52
2696 2732 6.644592 CCTTCTTTTCTGTAGAGACTTCACTG 59.355 42.308 0.00 0.00 0.00 3.66
2716 2752 0.251341 GGATGGTTGTGGTGCCTTCT 60.251 55.000 0.00 0.00 31.82 2.85
2730 2767 4.181010 CCACGAGCCCCTGGATGG 62.181 72.222 0.00 0.00 0.00 3.51
2738 2779 2.766651 TACCCCATCCACGAGCCC 60.767 66.667 0.00 0.00 0.00 5.19
2752 2793 1.382833 GGACCTCACCTCCCCTACC 60.383 68.421 0.00 0.00 0.00 3.18
2758 2799 1.481871 TGTATTCGGACCTCACCTCC 58.518 55.000 0.00 0.00 0.00 4.30
2806 2847 1.053835 TCACACACCCTTGGCTCTGA 61.054 55.000 0.00 0.00 0.00 3.27
2835 2876 5.994250 ACACTTGCCATGACTCTTACATAT 58.006 37.500 0.00 0.00 0.00 1.78
2836 2877 5.046663 TGACACTTGCCATGACTCTTACATA 60.047 40.000 0.00 0.00 0.00 2.29
2890 2935 0.698238 AGTCCCAATGCAGTGCCTTA 59.302 50.000 13.72 0.00 0.00 2.69
2898 2943 2.013563 GCATCGAGAAGTCCCAATGCA 61.014 52.381 0.00 0.00 39.36 3.96
2900 2945 1.667724 GTGCATCGAGAAGTCCCAATG 59.332 52.381 0.00 0.00 0.00 2.82
2946 2996 2.359230 GCCTCTGCCACCACACTC 60.359 66.667 0.00 0.00 0.00 3.51
2965 3015 1.393539 CTAACCGAGCATTCCAACACG 59.606 52.381 0.00 0.00 0.00 4.49
3000 3050 4.330944 ACAACGTCTCTCCACAAACATA 57.669 40.909 0.00 0.00 0.00 2.29
3002 3052 2.684001 ACAACGTCTCTCCACAAACA 57.316 45.000 0.00 0.00 0.00 2.83
3010 3060 3.913163 CCGAGAGTTTTACAACGTCTCTC 59.087 47.826 14.86 14.86 44.13 3.20
3017 3067 0.794473 CGCCCCGAGAGTTTTACAAC 59.206 55.000 0.00 0.00 0.00 3.32
3024 3093 2.282958 TCTCACGCCCCGAGAGTT 60.283 61.111 10.82 0.00 43.06 3.01
3026 3095 4.180946 CGTCTCACGCCCCGAGAG 62.181 72.222 5.85 5.85 43.68 3.20
3063 3132 1.374758 CACCTCCGTGCCTTCTGTC 60.375 63.158 0.00 0.00 32.04 3.51
3115 3184 0.877649 ATTGATAGCTGCTCGCACCG 60.878 55.000 4.91 0.00 42.61 4.94
3117 3186 0.506080 CGATTGATAGCTGCTCGCAC 59.494 55.000 4.91 0.00 42.61 5.34
3123 3192 1.939974 TCCACACGATTGATAGCTGC 58.060 50.000 0.00 0.00 0.00 5.25
3159 3228 1.203237 TTCGGAATCATGCCTCTGGA 58.797 50.000 0.00 0.00 0.00 3.86
3171 3240 2.696707 TCCCTAACTGCGTATTCGGAAT 59.303 45.455 8.49 8.49 36.90 3.01
3197 3266 3.096092 CTCTCTAGAGGCTTCACAACCT 58.904 50.000 19.67 0.00 38.48 3.50


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

AutoCloner maintained by Alex Coulton.