Multiple sequence alignment - TraesCS3D01G246800

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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 TraesCS3D01G246800 chr3D 100.000 5079 0 0 1 5079 346058923 346064001 0.000000e+00 9380.0
1 TraesCS3D01G246800 chr3D 93.802 597 37 0 4483 5079 350103905 350104501 0.000000e+00 898.0
2 TraesCS3D01G246800 chr3D 90.123 162 16 0 1250 1411 71499680 71499519 1.430000e-50 211.0
3 TraesCS3D01G246800 chr3D 74.834 151 30 7 501 645 592244631 592244779 1.530000e-05 62.1
4 TraesCS3D01G246800 chr3B 91.118 3648 172 40 879 4483 445201958 445205496 0.000000e+00 4802.0
5 TraesCS3D01G246800 chr3B 94.807 597 30 1 4483 5079 160433407 160434002 0.000000e+00 929.0
6 TraesCS3D01G246800 chr3B 89.709 447 17 10 452 898 445201527 445201944 1.240000e-150 544.0
7 TraesCS3D01G246800 chr3B 97.183 213 6 0 1 213 445201006 445201218 1.340000e-95 361.0
8 TraesCS3D01G246800 chr3B 90.741 162 15 0 1250 1411 117556907 117556746 3.080000e-52 217.0
9 TraesCS3D01G246800 chr3B 85.577 208 10 3 212 402 445201322 445201526 3.100000e-47 200.0
10 TraesCS3D01G246800 chr3A 93.487 2779 115 18 1732 4483 457664185 457661446 0.000000e+00 4069.0
11 TraesCS3D01G246800 chr3A 93.114 1249 49 14 440 1674 457665408 457664183 0.000000e+00 1796.0
12 TraesCS3D01G246800 chr3A 90.789 456 23 6 1 439 457665969 457665516 4.380000e-165 592.0
13 TraesCS3D01G246800 chr3A 89.595 173 18 0 1250 1422 83728197 83728025 2.380000e-53 220.0
14 TraesCS3D01G246800 chr1A 95.980 597 24 0 4483 5079 1782443 1781847 0.000000e+00 970.0
15 TraesCS3D01G246800 chr1A 85.753 365 38 11 1038 1401 539760006 539760357 1.730000e-99 374.0
16 TraesCS3D01G246800 chr1A 76.744 172 36 2 485 653 41781577 41781407 5.410000e-15 93.5
17 TraesCS3D01G246800 chr7A 95.142 597 29 0 4483 5079 309373539 309372943 0.000000e+00 942.0
18 TraesCS3D01G246800 chr5B 92.617 596 44 0 4483 5078 185520470 185521065 0.000000e+00 857.0
19 TraesCS3D01G246800 chr6A 91.275 596 52 0 4483 5078 563269683 563270278 0.000000e+00 813.0
20 TraesCS3D01G246800 chr5D 90.285 597 58 0 4483 5079 61375989 61376585 0.000000e+00 782.0
21 TraesCS3D01G246800 chr7B 89.280 597 64 0 4483 5079 723353979 723353383 0.000000e+00 749.0
22 TraesCS3D01G246800 chr7B 89.112 597 65 0 4483 5079 723231274 723230678 0.000000e+00 743.0
23 TraesCS3D01G246800 chr1B 82.426 404 41 16 1001 1401 603298821 603299197 4.900000e-85 326.0
24 TraesCS3D01G246800 chr1B 82.500 120 20 1 487 605 106384899 106385018 2.500000e-18 104.0
25 TraesCS3D01G246800 chr1D 83.516 364 36 14 1038 1401 443821436 443821775 8.210000e-83 318.0
26 TraesCS3D01G246800 chr1D 84.810 79 12 0 359 437 74341756 74341834 4.220000e-11 80.5
27 TraesCS3D01G246800 chr2D 81.102 127 17 5 443 564 115938314 115938438 1.510000e-15 95.3
28 TraesCS3D01G246800 chr6D 86.047 86 12 0 484 569 394215533 394215618 5.410000e-15 93.5
29 TraesCS3D01G246800 chr7D 80.899 89 17 0 481 569 171378279 171378367 2.540000e-08 71.3
30 TraesCS3D01G246800 chr7D 88.679 53 6 0 370 422 123322315 123322367 1.180000e-06 65.8
31 TraesCS3D01G246800 chr5A 84.615 65 10 0 359 423 631971688 631971752 1.180000e-06 65.8
32 TraesCS3D01G246800 chr6B 81.690 71 12 1 352 422 692488853 692488784 1.980000e-04 58.4


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 TraesCS3D01G246800 chr3D 346058923 346064001 5078 False 9380.000000 9380 100.000000 1 5079 1 chr3D.!!$F1 5078
1 TraesCS3D01G246800 chr3D 350103905 350104501 596 False 898.000000 898 93.802000 4483 5079 1 chr3D.!!$F2 596
2 TraesCS3D01G246800 chr3B 445201006 445205496 4490 False 1476.750000 4802 90.896750 1 4483 4 chr3B.!!$F2 4482
3 TraesCS3D01G246800 chr3B 160433407 160434002 595 False 929.000000 929 94.807000 4483 5079 1 chr3B.!!$F1 596
4 TraesCS3D01G246800 chr3A 457661446 457665969 4523 True 2152.333333 4069 92.463333 1 4483 3 chr3A.!!$R2 4482
5 TraesCS3D01G246800 chr1A 1781847 1782443 596 True 970.000000 970 95.980000 4483 5079 1 chr1A.!!$R1 596
6 TraesCS3D01G246800 chr7A 309372943 309373539 596 True 942.000000 942 95.142000 4483 5079 1 chr7A.!!$R1 596
7 TraesCS3D01G246800 chr5B 185520470 185521065 595 False 857.000000 857 92.617000 4483 5078 1 chr5B.!!$F1 595
8 TraesCS3D01G246800 chr6A 563269683 563270278 595 False 813.000000 813 91.275000 4483 5078 1 chr6A.!!$F1 595
9 TraesCS3D01G246800 chr5D 61375989 61376585 596 False 782.000000 782 90.285000 4483 5079 1 chr5D.!!$F1 596
10 TraesCS3D01G246800 chr7B 723353383 723353979 596 True 749.000000 749 89.280000 4483 5079 1 chr7B.!!$R2 596
11 TraesCS3D01G246800 chr7B 723230678 723231274 596 True 743.000000 743 89.112000 4483 5079 1 chr7B.!!$R1 596

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
733 968 0.613260 CGGACAGAAACCATGGAGGA 59.387 55.0 21.47 0.00 41.22 3.71 F
783 1018 0.666274 TCCTCTATTTATGCGCGCCG 60.666 55.0 30.77 7.99 0.00 6.46 F
1812 2122 0.575390 CAGTGTGGTTGTCGTTCGTC 59.425 55.0 0.00 0.00 0.00 4.20 F
2915 3240 0.106318 GCTTGGATTGCCTGGAGGAT 60.106 55.0 0.00 0.00 37.39 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1968 0.402887 CCCGGGTCCTGGTTAACTTT 59.597 55.000 14.18 0.0 0.00 2.66 R
1986 2300 0.528684 GGGAGATGTCGCTAGTGCAC 60.529 60.000 9.40 9.4 39.64 4.57 R
3810 4142 0.032615 AGATTCTCCAGCTCCTCCGT 60.033 55.000 0.00 0.0 0.00 4.69 R
4278 4613 1.566231 CCCCCATAGACAGCTTCCTTT 59.434 52.381 0.00 0.0 0.00 3.11 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
92 93 5.930569 AGTCATACTACCTTCGTTCCAAAAC 59.069 40.000 0.00 0.00 0.00 2.43
146 147 9.744468 ACTTTGACCAACAATTAGTGAAATAAC 57.256 29.630 0.00 0.00 38.36 1.89
304 407 1.136500 GAAACGGCGGAGGAGAGTATT 59.864 52.381 13.24 0.00 0.00 1.89
406 526 1.228154 GAAGGGCGTGTGGAGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
407 527 1.515521 GAAGGGCGTGTGGAGGTTTG 61.516 60.000 0.00 0.00 0.00 2.93
408 528 2.203294 GGGCGTGTGGAGGTTTGT 60.203 61.111 0.00 0.00 0.00 2.83
409 529 1.826487 GGGCGTGTGGAGGTTTGTT 60.826 57.895 0.00 0.00 0.00 2.83
464 691 3.119459 GGACTTAGCATGACGACTTCTCA 60.119 47.826 0.00 0.00 0.00 3.27
468 695 5.183331 ACTTAGCATGACGACTTCTCAACTA 59.817 40.000 0.00 0.00 0.00 2.24
479 706 5.120830 CGACTTCTCAACTATCTTTGTTGGG 59.879 44.000 6.75 3.79 44.67 4.12
556 789 7.488150 TGCTTCAGTGTTTATAGTCATCGTTAG 59.512 37.037 0.00 0.00 0.00 2.34
621 856 3.135225 TGTACAACCTTGACCGTTGATG 58.865 45.455 7.63 0.00 42.63 3.07
654 889 7.868415 TCAGACGTTTTTCCAGAAAAAGAAAAA 59.132 29.630 16.49 6.57 46.91 1.94
655 890 8.162245 CAGACGTTTTTCCAGAAAAAGAAAAAG 58.838 33.333 16.49 8.29 46.82 2.27
733 968 0.613260 CGGACAGAAACCATGGAGGA 59.387 55.000 21.47 0.00 41.22 3.71
783 1018 0.666274 TCCTCTATTTATGCGCGCCG 60.666 55.000 30.77 7.99 0.00 6.46
1020 1304 1.519455 GGTGGCGATCGAGAACCAG 60.519 63.158 21.57 0.00 31.46 4.00
1419 1709 2.932905 CGGGTACGTGCACAACAC 59.067 61.111 18.64 14.22 46.45 3.32
1429 1729 1.367665 GCACAACACAACGCGTCTC 60.368 57.895 14.44 0.00 0.00 3.36
1441 1741 3.531262 ACGCGTCTCAACAAAATAACC 57.469 42.857 5.58 0.00 0.00 2.85
1515 1817 3.711704 TCAGAACTGGTCTCCTCTGTTTT 59.288 43.478 0.00 0.00 37.25 2.43
1542 1844 4.664150 TTTTTGGGCGAACTTCTTTCAT 57.336 36.364 0.00 0.00 33.24 2.57
1551 1853 3.665323 CGAACTTCTTTCATGAACTGCCG 60.665 47.826 7.89 2.40 33.24 5.69
1556 1858 4.424061 TCTTTCATGAACTGCCGAATTG 57.576 40.909 7.89 0.00 0.00 2.32
1776 2086 1.069823 AGGAGATTCTACTGGCATGCG 59.930 52.381 12.44 0.62 0.00 4.73
1793 2103 1.332375 TGCGGCCGACTAATTTATTGC 59.668 47.619 33.48 6.37 0.00 3.56
1803 2113 5.794945 CGACTAATTTATTGCAGTGTGGTTG 59.205 40.000 0.00 0.00 0.00 3.77
1812 2122 0.575390 CAGTGTGGTTGTCGTTCGTC 59.425 55.000 0.00 0.00 0.00 4.20
1841 2151 1.230324 GCCGTGGGAATCTAGCATTC 58.770 55.000 6.44 6.44 0.00 2.67
1850 2160 7.857885 CGTGGGAATCTAGCATTCTAAAATTTC 59.142 37.037 11.96 0.00 0.00 2.17
1894 2207 9.745018 TCTTATCCATCAGTTCAGAAAGAAAAT 57.255 29.630 0.00 0.00 38.13 1.82
1929 2243 5.827797 GCCATTAGTCAATGAACTCCCATTA 59.172 40.000 0.00 0.00 43.67 1.90
1941 2255 5.648960 TGAACTCCCATTAAACCGGAATTAC 59.351 40.000 9.46 0.00 0.00 1.89
1948 2262 7.499895 TCCCATTAAACCGGAATTACTTATGTC 59.500 37.037 9.46 0.00 0.00 3.06
1949 2263 7.255346 CCCATTAAACCGGAATTACTTATGTCC 60.255 40.741 9.46 0.00 0.00 4.02
1950 2264 7.255346 CCATTAAACCGGAATTACTTATGTCCC 60.255 40.741 9.46 0.00 0.00 4.46
1951 2265 4.847990 AACCGGAATTACTTATGTCCCA 57.152 40.909 9.46 0.00 0.00 4.37
1978 2292 3.057033 TGTGACTTAGTCGAAAGCTACCC 60.057 47.826 7.92 0.00 34.95 3.69
1986 2300 3.564225 AGTCGAAAGCTACCCTTTGTTTG 59.436 43.478 0.00 0.00 43.64 2.93
2083 2403 9.777297 ATCTCTCTTCCTTAGATTATTTCTTGC 57.223 33.333 0.00 0.00 35.79 4.01
2087 2407 6.828785 TCTTCCTTAGATTATTTCTTGCCACC 59.171 38.462 0.00 0.00 35.79 4.61
2238 2558 1.597742 TGACTTGAGAAAGCAGGCAC 58.402 50.000 0.00 0.00 0.00 5.01
2404 2729 4.421948 CCGTAGCACGTTCTAGATTCTTT 58.578 43.478 0.00 0.00 40.58 2.52
2457 2782 9.627123 TCATAAATAAAAGGGAGTATCTTGTGG 57.373 33.333 0.00 0.00 33.73 4.17
2552 2877 4.949856 GCTGTCCTTGGAAAATGATAGGAA 59.050 41.667 0.00 0.00 36.80 3.36
2615 2940 8.812329 TGTAAACACAAACTAATGCAAATGTTC 58.188 29.630 0.00 0.00 0.00 3.18
2751 3076 2.257207 TGGGACAGACTGAAGTAAGGG 58.743 52.381 10.08 0.00 0.00 3.95
2915 3240 0.106318 GCTTGGATTGCCTGGAGGAT 60.106 55.000 0.00 0.00 37.39 3.24
3057 3382 6.110543 TCATTGTGAGTTTCTATGCATTCG 57.889 37.500 3.54 0.00 0.00 3.34
3108 3433 6.767524 TTGGTGTATGGAAATCATGTAACC 57.232 37.500 0.00 0.00 37.30 2.85
3109 3434 6.073447 TGGTGTATGGAAATCATGTAACCT 57.927 37.500 0.00 0.00 36.11 3.50
3110 3435 6.119536 TGGTGTATGGAAATCATGTAACCTC 58.880 40.000 0.00 0.00 36.11 3.85
3111 3436 6.069673 TGGTGTATGGAAATCATGTAACCTCT 60.070 38.462 0.00 0.00 36.11 3.69
3112 3437 6.483640 GGTGTATGGAAATCATGTAACCTCTC 59.516 42.308 0.00 0.00 37.30 3.20
3113 3438 7.275920 GTGTATGGAAATCATGTAACCTCTCT 58.724 38.462 0.00 0.00 37.30 3.10
3114 3439 7.770897 GTGTATGGAAATCATGTAACCTCTCTT 59.229 37.037 0.00 0.00 37.30 2.85
3115 3440 8.988060 TGTATGGAAATCATGTAACCTCTCTTA 58.012 33.333 0.00 0.00 37.30 2.10
3116 3441 9.832445 GTATGGAAATCATGTAACCTCTCTTAA 57.168 33.333 0.00 0.00 37.30 1.85
3118 3443 9.753674 ATGGAAATCATGTAACCTCTCTTAAAA 57.246 29.630 0.00 0.00 34.22 1.52
3119 3444 9.581289 TGGAAATCATGTAACCTCTCTTAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
3176 3502 1.429463 CACGTTGGTAGGCTGAACTC 58.571 55.000 0.00 0.00 0.00 3.01
3230 3557 3.183775 CAGTTTTGTTCCTTACGACTCGG 59.816 47.826 2.98 0.00 0.00 4.63
3252 3579 0.251653 TCCTAAGGTGTCACGCCTCT 60.252 55.000 11.28 3.87 44.35 3.69
3260 3587 3.514309 AGGTGTCACGCCTCTACTAAAAT 59.486 43.478 3.22 0.00 40.81 1.82
3337 3664 6.043854 TCTTGTTGTATATGCTGTGTACCA 57.956 37.500 0.00 0.00 0.00 3.25
3348 3675 0.251121 TGTGTACCAACCTGCCATGG 60.251 55.000 7.63 7.63 42.60 3.66
3371 3698 5.412904 GGGTCATGACAGTTTCTTAAGGAAG 59.587 44.000 26.47 0.00 35.16 3.46
3396 3723 6.371825 GTCTGAAGTTTTATCCCACCTTGTAG 59.628 42.308 0.00 0.00 0.00 2.74
3404 3731 0.598065 CCCACCTTGTAGCAAACTGC 59.402 55.000 0.00 0.00 45.46 4.40
3416 3743 2.240667 AGCAAACTGCCAGACATCCTAT 59.759 45.455 0.00 0.00 46.52 2.57
3527 3854 3.937814 TGACATCGCTAACCATTTCTGT 58.062 40.909 0.00 0.00 0.00 3.41
3611 3938 7.330262 CAGGTATTGCATTTCCCATTTAACTT 58.670 34.615 1.09 0.00 0.00 2.66
3619 3946 6.648725 GCATTTCCCATTTAACTTTGCTTGTA 59.351 34.615 0.00 0.00 0.00 2.41
3640 3967 1.878953 TTTCGTTCAGCCTTCACTCC 58.121 50.000 0.00 0.00 0.00 3.85
3642 3969 0.318441 TCGTTCAGCCTTCACTCCAG 59.682 55.000 0.00 0.00 0.00 3.86
3658 3990 7.435068 TCACTCCAGCTTATTTGTTAACTTC 57.565 36.000 7.22 0.00 0.00 3.01
3659 3991 7.224297 TCACTCCAGCTTATTTGTTAACTTCT 58.776 34.615 7.22 0.00 0.00 2.85
3680 4012 2.071688 ATTCTGCGGCAGATATCGAC 57.928 50.000 31.20 0.00 40.39 4.20
3731 4063 3.255888 TGAGCACTTCTCGTGAGTACAAT 59.744 43.478 0.00 0.00 46.81 2.71
3736 4068 9.935094 GAGCACTTCTCGTGAGTACAATACTCC 62.935 48.148 12.33 4.60 46.81 3.85
3763 4095 0.387622 TGGTTCGATTGTCCGACGAC 60.388 55.000 0.00 0.00 38.39 4.34
3771 4103 1.034356 TTGTCCGACGACTCCTTTCA 58.966 50.000 0.00 0.00 39.94 2.69
3781 4113 5.593010 GACGACTCCTTTCATGCTAATACT 58.407 41.667 0.00 0.00 0.00 2.12
3782 4114 5.978814 ACGACTCCTTTCATGCTAATACTT 58.021 37.500 0.00 0.00 0.00 2.24
3819 4151 0.673956 GGAACCTGAAACGGAGGAGC 60.674 60.000 0.00 0.00 34.37 4.70
3896 4228 2.919602 GGGCCTCTGGGGAATAATATCA 59.080 50.000 0.84 0.00 37.23 2.15
3919 4251 2.167693 TGAGTTCATATTCGGGTTCGCT 59.832 45.455 0.00 0.00 36.13 4.93
3936 4268 1.394917 CGCTAACCAAGTCATGACTGC 59.605 52.381 28.52 22.90 41.58 4.40
3967 4299 3.060873 GCGCTGCTATCTTCTAACTTTCG 60.061 47.826 0.00 0.00 0.00 3.46
3993 4325 5.465390 TGTTTTCTTTACAGGATCGTGTCAG 59.535 40.000 23.41 19.26 31.46 3.51
3994 4326 4.866508 TTCTTTACAGGATCGTGTCAGT 57.133 40.909 23.41 3.04 31.46 3.41
4093 4425 7.380423 AACCTCATGAATAGCTGTACCTATT 57.620 36.000 0.00 4.59 39.92 1.73
4125 4460 4.031129 CTGAGGGCCTGTGCTGCT 62.031 66.667 12.95 0.00 37.74 4.24
4126 4461 4.340246 TGAGGGCCTGTGCTGCTG 62.340 66.667 12.95 0.00 37.74 4.41
4194 4529 6.562223 TGGGATAATGACAGGAAGGATATGAA 59.438 38.462 0.00 0.00 0.00 2.57
4278 4613 1.423584 TGACAAGGTCCAGCTTCAGA 58.576 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.323985 GACTTCTTATCTACTTTGAGATTGCAT 57.676 33.333 0.00 0.00 37.38 3.96
271 374 4.453136 TCCGCCGTTTCATAATATAAAGCC 59.547 41.667 0.00 0.00 0.00 4.35
304 407 9.589461 TTAGTAGGGAACAAAATGGACAAAATA 57.411 29.630 0.00 0.00 0.00 1.40
366 486 0.888736 CAACGCTGGAATCACCACCA 60.889 55.000 0.00 0.00 44.64 4.17
406 526 1.067142 CCTCAAGATCCGACGGAAACA 60.067 52.381 22.55 0.00 34.34 2.83
407 527 1.641577 CCTCAAGATCCGACGGAAAC 58.358 55.000 22.55 17.46 34.34 2.78
408 528 0.535335 CCCTCAAGATCCGACGGAAA 59.465 55.000 22.55 0.00 34.34 3.13
409 529 0.323999 TCCCTCAAGATCCGACGGAA 60.324 55.000 22.55 2.40 34.34 4.30
521 748 1.035139 ACACTGAAGCAAGCCAAAGG 58.965 50.000 0.00 0.00 0.00 3.11
522 749 2.877043 AACACTGAAGCAAGCCAAAG 57.123 45.000 0.00 0.00 0.00 2.77
523 750 4.935352 ATAAACACTGAAGCAAGCCAAA 57.065 36.364 0.00 0.00 0.00 3.28
524 751 5.070001 ACTATAAACACTGAAGCAAGCCAA 58.930 37.500 0.00 0.00 0.00 4.52
525 752 4.651778 ACTATAAACACTGAAGCAAGCCA 58.348 39.130 0.00 0.00 0.00 4.75
556 789 7.908453 AGTTATATTTAGGTCCATAGAGCACC 58.092 38.462 0.00 0.00 43.21 5.01
654 889 4.266714 TGAGTCGTTGTTTTCCTTTTCCT 58.733 39.130 0.00 0.00 0.00 3.36
655 890 4.625972 TGAGTCGTTGTTTTCCTTTTCC 57.374 40.909 0.00 0.00 0.00 3.13
656 891 4.494410 CGTTGAGTCGTTGTTTTCCTTTTC 59.506 41.667 0.00 0.00 0.00 2.29
733 968 1.388133 GGGGGTTTTCCAGATGCCT 59.612 57.895 0.00 0.00 42.91 4.75
783 1018 3.094484 TGGGATGGTTTATGTGGTTCC 57.906 47.619 0.00 0.00 0.00 3.62
860 1095 7.233757 AGCGAGATTGGATATAAAGAACTAGGT 59.766 37.037 0.00 0.00 0.00 3.08
1045 1329 4.241555 CTTGGGGATCCTCGCGGG 62.242 72.222 12.58 0.59 0.00 6.13
1416 1706 1.080298 TTTGTTGAGACGCGTTGTGT 58.920 45.000 15.53 0.00 0.00 3.72
1417 1707 2.166741 TTTTGTTGAGACGCGTTGTG 57.833 45.000 15.53 0.00 0.00 3.33
1418 1708 4.276460 GTTATTTTGTTGAGACGCGTTGT 58.724 39.130 15.53 3.35 0.00 3.32
1419 1709 3.662186 GGTTATTTTGTTGAGACGCGTTG 59.338 43.478 15.53 0.00 0.00 4.10
1429 1729 9.277565 CGATTTGATAGAGTGGTTATTTTGTTG 57.722 33.333 0.00 0.00 0.00 3.33
1441 1741 7.602517 AAGGAAGAAACGATTTGATAGAGTG 57.397 36.000 0.00 0.00 0.00 3.51
1454 1754 6.253512 CCAAGAAAAACTGAAAGGAAGAAACG 59.746 38.462 0.00 0.00 39.30 3.60
1521 1823 4.098654 TCATGAAAGAAGTTCGCCCAAAAA 59.901 37.500 0.00 0.00 39.30 1.94
1522 1824 3.634448 TCATGAAAGAAGTTCGCCCAAAA 59.366 39.130 0.00 0.00 39.30 2.44
1523 1825 3.218453 TCATGAAAGAAGTTCGCCCAAA 58.782 40.909 0.00 0.00 39.30 3.28
1524 1826 2.857483 TCATGAAAGAAGTTCGCCCAA 58.143 42.857 0.00 0.00 39.30 4.12
1525 1827 2.552315 GTTCATGAAAGAAGTTCGCCCA 59.448 45.455 10.35 0.00 39.30 5.36
1526 1828 2.814336 AGTTCATGAAAGAAGTTCGCCC 59.186 45.455 10.35 0.00 39.30 6.13
1533 1835 4.691860 ATTCGGCAGTTCATGAAAGAAG 57.308 40.909 10.35 1.69 0.00 2.85
1541 1843 1.741706 CAGAGCAATTCGGCAGTTCAT 59.258 47.619 0.00 0.00 35.83 2.57
1542 1844 1.159285 CAGAGCAATTCGGCAGTTCA 58.841 50.000 0.00 0.00 35.83 3.18
1551 1853 7.195839 ACTCTTACAGAAAACAGAGCAATTC 57.804 36.000 0.00 0.00 36.95 2.17
1556 1858 7.472543 TGAAAAACTCTTACAGAAAACAGAGC 58.527 34.615 0.00 0.00 36.95 4.09
1664 1967 1.629861 CCCGGGTCCTGGTTAACTTTA 59.370 52.381 14.18 0.00 0.00 1.85
1665 1968 0.402887 CCCGGGTCCTGGTTAACTTT 59.597 55.000 14.18 0.00 0.00 2.66
1776 2086 3.377172 ACACTGCAATAAATTAGTCGGCC 59.623 43.478 0.00 0.00 0.00 6.13
1793 2103 0.575390 GACGAACGACAACCACACTG 59.425 55.000 0.14 0.00 0.00 3.66
1812 2122 0.953471 TTCCCACGGCAGAACATTCG 60.953 55.000 0.00 0.00 0.00 3.34
1863 2173 9.658799 CTTTCTGAACTGATGGATAAGACTAAA 57.341 33.333 0.00 0.00 0.00 1.85
1864 2174 9.035890 TCTTTCTGAACTGATGGATAAGACTAA 57.964 33.333 0.00 0.00 0.00 2.24
1894 2207 8.806429 TCATTGACTAATGGCTTGAAGAAATA 57.194 30.769 0.00 0.00 43.11 1.40
1895 2208 7.707624 TCATTGACTAATGGCTTGAAGAAAT 57.292 32.000 0.00 0.00 43.11 2.17
1896 2209 7.231317 AGTTCATTGACTAATGGCTTGAAGAAA 59.769 33.333 0.00 0.00 43.11 2.52
1929 2243 4.945543 GTGGGACATAAGTAATTCCGGTTT 59.054 41.667 0.00 0.00 44.52 3.27
1948 2262 1.405526 CGACTAAGTCACATGGGTGGG 60.406 57.143 0.00 0.00 45.32 4.61
1949 2263 1.548719 TCGACTAAGTCACATGGGTGG 59.451 52.381 0.00 0.00 45.32 4.61
1950 2264 3.313012 TTCGACTAAGTCACATGGGTG 57.687 47.619 0.00 0.00 46.66 4.61
1951 2265 3.864921 GCTTTCGACTAAGTCACATGGGT 60.865 47.826 0.00 0.00 32.09 4.51
1978 2292 2.031560 TGTCGCTAGTGCACAAACAAAG 59.968 45.455 21.04 7.23 39.64 2.77
1986 2300 0.528684 GGGAGATGTCGCTAGTGCAC 60.529 60.000 9.40 9.40 39.64 4.57
2083 2403 3.756434 ACACCACAAATTTATCGAGGTGG 59.244 43.478 20.18 18.80 46.93 4.61
2087 2407 6.073276 TGACTTCACACCACAAATTTATCGAG 60.073 38.462 0.00 0.00 0.00 4.04
2238 2558 3.244033 TGTTTTGCCAACTTGGTCTTG 57.756 42.857 9.63 0.00 40.46 3.02
2404 2729 5.051039 GCGACGCAAATAATGAAGTGATCTA 60.051 40.000 16.42 0.00 0.00 1.98
2457 2782 0.741915 TTGTTCGCCCCAGAAAACAC 59.258 50.000 0.00 0.00 31.76 3.32
2552 2877 2.024464 TGGCCACCTTGGTAGCAAATAT 60.024 45.455 0.00 0.00 40.46 1.28
2615 2940 1.493311 GCCGACAGCGTCTGAAAAG 59.507 57.895 12.77 1.83 35.18 2.27
2751 3076 6.642131 TCATTTGTGCAAGAACTAAAGATTGC 59.358 34.615 0.00 1.96 46.36 3.56
2861 3186 0.035820 GATCGGTTGGGCACAGGTTA 60.036 55.000 0.00 0.00 0.00 2.85
2915 3240 2.440247 TCCAGCGAGGCGATCTCA 60.440 61.111 6.94 0.00 42.55 3.27
2936 3261 3.435169 GGTGGTAATCCCCTGAGAATTCC 60.435 52.174 0.65 0.00 0.00 3.01
3121 3446 9.122779 CCCCATTTGCATATTTTACATGATTTT 57.877 29.630 0.00 0.00 0.00 1.82
3122 3447 8.492782 TCCCCATTTGCATATTTTACATGATTT 58.507 29.630 0.00 0.00 0.00 2.17
3176 3502 3.349927 TGCATGAGATGAGAAACTTGGG 58.650 45.455 0.00 0.00 0.00 4.12
3230 3557 1.090052 GGCGTGACACCTTAGGATGC 61.090 60.000 4.77 0.00 0.00 3.91
3260 3587 6.072618 CGTACTCTCCAAGACTAAAACTCTGA 60.073 42.308 0.00 0.00 0.00 3.27
3337 3664 0.323725 GTCATGACCCATGGCAGGTT 60.324 55.000 15.31 0.00 44.75 3.50
3348 3675 5.998363 ACTTCCTTAAGAAACTGTCATGACC 59.002 40.000 22.85 7.15 36.50 4.02
3371 3698 5.070685 ACAAGGTGGGATAAAACTTCAGAC 58.929 41.667 0.00 0.00 0.00 3.51
3396 3723 2.113860 TAGGATGTCTGGCAGTTTGC 57.886 50.000 15.27 5.99 44.08 3.68
3404 3731 7.423844 TGCCAACTATATATAGGATGTCTGG 57.576 40.000 21.20 16.62 34.69 3.86
3416 3743 8.052748 AGATCAAACCAACTTGCCAACTATATA 58.947 33.333 0.00 0.00 0.00 0.86
3527 3854 1.676678 GGTAGTCTGCCGCCATCTCA 61.677 60.000 0.00 0.00 0.00 3.27
3611 3938 3.568007 AGGCTGAACGAAAATACAAGCAA 59.432 39.130 0.00 0.00 0.00 3.91
3619 3946 2.814336 GGAGTGAAGGCTGAACGAAAAT 59.186 45.455 0.00 0.00 0.00 1.82
3642 3969 9.000018 CGCAGAATAAGAAGTTAACAAATAAGC 58.000 33.333 8.61 0.00 0.00 3.09
3658 3990 3.610242 GTCGATATCTGCCGCAGAATAAG 59.390 47.826 26.30 17.37 44.04 1.73
3659 3991 3.575630 GTCGATATCTGCCGCAGAATAA 58.424 45.455 26.30 15.17 44.04 1.40
3680 4012 2.430921 ACGAAACGCCTCTGCTCG 60.431 61.111 0.00 0.00 38.30 5.03
3731 4063 6.884832 ACAATCGAACCAAGATAATGGAGTA 58.115 36.000 0.00 0.00 43.54 2.59
3736 4068 4.808895 TCGGACAATCGAACCAAGATAATG 59.191 41.667 0.00 0.00 36.12 1.90
3763 4095 8.273780 ACAAAGAAGTATTAGCATGAAAGGAG 57.726 34.615 0.00 0.00 0.00 3.69
3771 4103 5.016173 TGCCCAACAAAGAAGTATTAGCAT 58.984 37.500 0.00 0.00 0.00 3.79
3781 4113 1.152860 TCGCCTGCCCAACAAAGAA 60.153 52.632 0.00 0.00 0.00 2.52
3782 4114 1.600636 CTCGCCTGCCCAACAAAGA 60.601 57.895 0.00 0.00 0.00 2.52
3810 4142 0.032615 AGATTCTCCAGCTCCTCCGT 60.033 55.000 0.00 0.00 0.00 4.69
3896 4228 3.782046 CGAACCCGAATATGAACTCACT 58.218 45.455 0.00 0.00 38.22 3.41
3919 4251 4.650734 TGATTGCAGTCATGACTTGGTTA 58.349 39.130 25.84 10.03 40.20 2.85
3924 4256 4.024302 CGCATATGATTGCAGTCATGACTT 60.024 41.667 29.08 11.66 42.91 3.01
3931 4263 1.662309 GCAGCGCATATGATTGCAGTC 60.662 52.381 11.47 1.56 42.91 3.51
3936 4268 4.630505 AGAAGATAGCAGCGCATATGATTG 59.369 41.667 11.47 0.00 0.00 2.67
3967 4299 6.056428 ACACGATCCTGTAAAGAAAACAAC 57.944 37.500 0.00 0.00 0.00 3.32
4194 4529 7.338710 TGCTTCCTTGTAATAGTATGCTTCTT 58.661 34.615 0.00 0.00 0.00 2.52
4278 4613 1.566231 CCCCCATAGACAGCTTCCTTT 59.434 52.381 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.