Multiple sequence alignment - TraesCS4D01G314100

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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 TraesCS4D01G314100 chr4D 100.000 2945 0 0 1 2945 479963430 479960486 0.000000e+00 5439.0
1 TraesCS4D01G314100 chr4D 87.549 257 22 6 298 545 465910072 465909817 3.710000e-74 289.0
2 TraesCS4D01G314100 chr4D 93.043 115 8 0 112 226 465910159 465910045 5.050000e-38 169.0
3 TraesCS4D01G314100 chr4D 91.781 73 6 0 181 253 479963184 479963112 5.190000e-18 102.0
4 TraesCS4D01G314100 chr4D 91.781 73 6 0 247 319 479963250 479963178 5.190000e-18 102.0
5 TraesCS4D01G314100 chr4B 93.867 1386 42 17 1565 2945 607287436 607286089 0.000000e+00 2049.0
6 TraesCS4D01G314100 chr4B 87.387 1443 70 35 197 1564 607288926 607287521 0.000000e+00 1554.0
7 TraesCS4D01G314100 chr4B 92.560 336 14 2 1 325 607289265 607288930 3.440000e-129 472.0
8 TraesCS4D01G314100 chr4B 91.667 132 11 0 189 320 607289000 607288869 1.800000e-42 183.0
9 TraesCS4D01G314100 chr4B 94.118 68 4 0 253 320 607289068 607289001 1.440000e-18 104.0
10 TraesCS4D01G314100 chr4A 91.236 696 39 3 2271 2945 686384029 686383335 0.000000e+00 928.0
11 TraesCS4D01G314100 chr4A 86.646 659 43 20 1672 2306 686384666 686384029 0.000000e+00 688.0
12 TraesCS4D01G314100 chr4A 89.968 309 20 9 247 545 641601657 641601964 3.560000e-104 388.0
13 TraesCS4D01G314100 chr4A 79.661 590 67 31 920 1487 686385703 686385145 2.770000e-100 375.0
14 TraesCS4D01G314100 chr4A 75.224 670 91 51 921 1563 641610544 641611165 6.300000e-62 248.0
15 TraesCS4D01G314100 chr4A 91.160 181 12 3 76 253 641601550 641601729 2.930000e-60 243.0
16 TraesCS4D01G314100 chr4A 82.812 192 15 8 1955 2145 641610152 641610326 3.930000e-34 156.0
17 TraesCS4D01G314100 chr6D 79.383 713 81 36 871 1564 446489079 446489744 2.690000e-120 442.0
18 TraesCS4D01G314100 chr6D 90.756 119 6 3 1904 2018 446490610 446490727 1.410000e-33 154.0
19 TraesCS4D01G314100 chr6D 92.308 52 2 1 1672 1723 446489875 446489924 4.070000e-09 73.1
20 TraesCS4D01G314100 chr6D 87.931 58 6 1 1724 1780 446489942 446489999 1.890000e-07 67.6
21 TraesCS4D01G314100 chr2B 82.745 510 62 16 908 1403 572586369 572586866 5.830000e-117 431.0
22 TraesCS4D01G314100 chr2B 79.046 482 67 20 911 1376 701491107 701490644 1.720000e-77 300.0
23 TraesCS4D01G314100 chr2B 87.786 131 13 3 1949 2078 572585825 572585953 1.830000e-32 150.0
24 TraesCS4D01G314100 chr2B 85.593 118 7 6 2081 2188 572587450 572587567 6.670000e-22 115.0
25 TraesCS4D01G314100 chr2B 92.308 65 4 1 2670 2733 572587597 572587661 1.120000e-14 91.6
26 TraesCS4D01G314100 chr5A 80.361 499 76 14 908 1403 456485748 456485269 2.790000e-95 359.0
27 TraesCS4D01G314100 chr5A 90.303 165 11 5 1983 2144 474537999 474537837 8.270000e-51 211.0
28 TraesCS4D01G314100 chr5A 84.332 217 20 7 1937 2147 456492541 456492333 1.790000e-47 200.0
29 TraesCS4D01G314100 chr2D 80.503 477 63 18 911 1376 582495018 582494561 3.640000e-89 339.0
30 TraesCS4D01G314100 chr2D 80.313 447 44 24 954 1377 488229103 488229528 6.170000e-77 298.0
31 TraesCS4D01G314100 chr2D 97.222 36 1 0 2822 2857 488230780 488230815 8.810000e-06 62.1
32 TraesCS4D01G314100 chr6A 87.625 299 22 11 1723 2018 593354452 593354738 1.690000e-87 333.0
33 TraesCS4D01G314100 chr5B 79.907 428 51 18 966 1376 448804033 448803624 6.210000e-72 281.0
34 TraesCS4D01G314100 chr5B 84.286 140 12 5 1939 2076 441441870 441441739 8.570000e-26 128.0
35 TraesCS4D01G314100 chr6B 83.607 305 17 11 1672 1955 674936111 674936403 3.770000e-64 255.0
36 TraesCS4D01G314100 chr6B 90.323 62 5 1 1957 2018 674936491 674936551 2.430000e-11 80.5
37 TraesCS4D01G314100 chr2A 88.406 207 19 3 2568 2773 632623663 632623865 8.150000e-61 244.0
38 TraesCS4D01G314100 chr2A 100.000 32 0 0 1950 1981 632612975 632613006 3.170000e-05 60.2
39 TraesCS4D01G314100 chr5D 86.175 217 16 7 1937 2147 371441357 371441149 3.820000e-54 222.0
40 TraesCS4D01G314100 chr7B 87.640 89 7 2 2 86 630652355 630652267 1.870000e-17 100.0
41 TraesCS4D01G314100 chr7D 88.608 79 9 0 5 83 572836007 572835929 2.420000e-16 97.1


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 TraesCS4D01G314100 chr4D 479960486 479963430 2944 True 1881.000000 5439 94.520667 1 2945 3 chr4D.!!$R2 2944
1 TraesCS4D01G314100 chr4B 607286089 607289265 3176 True 872.400000 2049 91.919800 1 2945 5 chr4B.!!$R1 2944
2 TraesCS4D01G314100 chr4A 686383335 686385703 2368 True 663.666667 928 85.847667 920 2945 3 chr4A.!!$R1 2025
3 TraesCS4D01G314100 chr4A 641610152 641611165 1013 False 202.000000 248 79.018000 921 2145 2 chr4A.!!$F2 1224

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
526 670 0.184692 TTTGGTGTCCATGGCACTCA 59.815 50.0 27.36 22.26 37.07 3.41 F
1014 1210 0.175302 CCACCAAAGCAACACAAGCA 59.825 50.0 0.00 0.00 0.00 3.91 F
1806 2484 0.037975 CCCCAACAATGCTGCTTCAC 60.038 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 2426 0.607620 GCAATTGCAGGCCTACCAAA 59.392 50.000 25.36 6.58 41.59 3.28 R
1897 2575 0.657368 CTGGTTCGTTCGTTTGCTGC 60.657 55.000 0.00 0.00 0.00 5.25 R
2665 3391 2.801342 GCAGATTGAAACCGCAAAACCA 60.801 45.455 0.00 0.00 0.00 3.67 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
57 61 7.707035 ACCTAAACTAATTATCAGCGACAGAAG 59.293 37.037 0.00 0.00 0.00 2.85
309 387 2.879907 GTAGTGTACTCGCCGGCA 59.120 61.111 28.98 12.94 0.00 5.69
462 606 2.771762 AGCATGGCCTCCTCCTCC 60.772 66.667 3.32 0.00 0.00 4.30
519 663 1.308069 CCGCTCCTTTGGTGTCCATG 61.308 60.000 0.00 0.00 31.53 3.66
526 670 0.184692 TTTGGTGTCCATGGCACTCA 59.815 50.000 27.36 22.26 37.07 3.41
560 704 3.133721 GGGCTTGCTAGAGAGATCAAAGA 59.866 47.826 0.00 0.00 0.00 2.52
576 735 5.296151 TCAAAGAATGCTAGGGAATCGAT 57.704 39.130 0.00 0.00 0.00 3.59
586 745 2.235016 AGGGAATCGATCGAGAAGAGG 58.765 52.381 23.84 0.00 0.00 3.69
589 748 2.389998 GAATCGATCGAGAAGAGGTGC 58.610 52.381 23.84 0.00 0.00 5.01
596 755 2.307768 TCGAGAAGAGGTGCGGATATT 58.692 47.619 0.00 0.00 0.00 1.28
603 762 0.816825 AGGTGCGGATATTGCTGCTG 60.817 55.000 0.00 0.00 40.79 4.41
604 763 1.009222 GTGCGGATATTGCTGCTGC 60.009 57.895 8.89 8.89 40.79 5.25
605 764 2.250485 GCGGATATTGCTGCTGCG 59.750 61.111 11.21 0.00 43.34 5.18
606 765 2.941333 CGGATATTGCTGCTGCGG 59.059 61.111 11.21 3.55 43.34 5.69
607 766 2.641559 GGATATTGCTGCTGCGGC 59.358 61.111 25.96 25.96 43.34 6.53
608 767 1.895707 GGATATTGCTGCTGCGGCT 60.896 57.895 31.19 16.70 43.34 5.52
609 768 0.603707 GGATATTGCTGCTGCGGCTA 60.604 55.000 31.19 25.42 43.34 3.93
610 769 1.446907 GATATTGCTGCTGCGGCTAT 58.553 50.000 31.19 29.50 43.34 2.97
611 770 1.129998 GATATTGCTGCTGCGGCTATG 59.870 52.381 31.21 10.05 43.34 2.23
612 771 0.886043 TATTGCTGCTGCGGCTATGG 60.886 55.000 31.21 7.48 43.34 2.74
613 772 4.862447 TGCTGCTGCGGCTATGGG 62.862 66.667 31.19 4.99 43.34 4.00
615 774 4.181010 CTGCTGCGGCTATGGGGT 62.181 66.667 20.27 0.00 39.59 4.95
616 775 4.488136 TGCTGCGGCTATGGGGTG 62.488 66.667 20.27 0.00 39.59 4.61
658 817 4.494811 GCAGGGGCGTTTTATTGC 57.505 55.556 0.00 0.00 0.00 3.56
659 818 1.890174 GCAGGGGCGTTTTATTGCT 59.110 52.632 0.00 0.00 0.00 3.91
660 819 0.246360 GCAGGGGCGTTTTATTGCTT 59.754 50.000 0.00 0.00 0.00 3.91
664 823 1.816224 GGGGCGTTTTATTGCTTGAGA 59.184 47.619 0.00 0.00 0.00 3.27
706 865 1.377333 GGGACAAGGAAGAAGCGGG 60.377 63.158 0.00 0.00 0.00 6.13
724 883 4.200283 GAGGACGAGCAGCTCCCG 62.200 72.222 17.16 9.41 0.00 5.14
727 886 2.507324 GACGAGCAGCTCCCGTTC 60.507 66.667 17.16 4.69 36.60 3.95
741 900 1.440938 CCGTTCCCGTTTGCACTTGA 61.441 55.000 0.00 0.00 0.00 3.02
745 904 2.270352 TCCCGTTTGCACTTGAGATT 57.730 45.000 0.00 0.00 0.00 2.40
746 905 1.879380 TCCCGTTTGCACTTGAGATTG 59.121 47.619 0.00 0.00 0.00 2.67
751 910 4.083110 CCGTTTGCACTTGAGATTGAGATT 60.083 41.667 0.00 0.00 0.00 2.40
760 919 8.838365 GCACTTGAGATTGAGATTATCTTCATT 58.162 33.333 0.00 0.00 32.64 2.57
763 922 9.473640 CTTGAGATTGAGATTATCTTCATTCGA 57.526 33.333 0.00 0.00 32.64 3.71
764 923 9.993454 TTGAGATTGAGATTATCTTCATTCGAT 57.007 29.630 0.00 0.00 32.64 3.59
765 924 9.636879 TGAGATTGAGATTATCTTCATTCGATC 57.363 33.333 0.00 0.00 32.64 3.69
790 949 8.122952 TCATCAGAAAAGAAAAGAGTTCGTTTC 58.877 33.333 15.27 15.27 42.82 2.78
814 995 1.069668 GTGGTACTTCCTCGTGTGGTT 59.930 52.381 0.00 0.00 37.07 3.67
918 1114 1.070786 GTCCAAGTCCAAGTCCGCA 59.929 57.895 0.00 0.00 0.00 5.69
945 1141 0.321671 CGGCTTCCTCCTCAAGACAA 59.678 55.000 0.00 0.00 0.00 3.18
947 1143 1.625818 GGCTTCCTCCTCAAGACAAGA 59.374 52.381 0.00 0.00 0.00 3.02
949 1145 2.614229 GCTTCCTCCTCAAGACAAGACC 60.614 54.545 0.00 0.00 0.00 3.85
950 1146 2.704190 TCCTCCTCAAGACAAGACCT 57.296 50.000 0.00 0.00 0.00 3.85
951 1147 2.530701 TCCTCCTCAAGACAAGACCTC 58.469 52.381 0.00 0.00 0.00 3.85
952 1148 1.552792 CCTCCTCAAGACAAGACCTCC 59.447 57.143 0.00 0.00 0.00 4.30
981 1177 2.287970 TGCATATAAGTAGGCACGACCG 60.288 50.000 0.00 0.00 42.14 4.79
1012 1208 0.530431 GGCCACCAAAGCAACACAAG 60.530 55.000 0.00 0.00 0.00 3.16
1014 1210 0.175302 CCACCAAAGCAACACAAGCA 59.825 50.000 0.00 0.00 0.00 3.91
1015 1211 1.563111 CACCAAAGCAACACAAGCAG 58.437 50.000 0.00 0.00 0.00 4.24
1064 1261 4.849926 TGACGTAGAAAGTTTTCGATCTCG 59.150 41.667 12.96 0.00 41.92 4.04
1260 1493 1.604278 GTGCCTCAAGAACAAGGTCAC 59.396 52.381 0.00 0.00 34.73 3.67
1271 1504 1.073923 ACAAGGTCACCTCCATGTTCC 59.926 52.381 0.00 0.00 36.21 3.62
1599 2246 7.081526 AGATGTGCACTTTATCTGTCAAATC 57.918 36.000 19.41 7.57 30.41 2.17
1602 2249 7.601073 TGTGCACTTTATCTGTCAAATCTAG 57.399 36.000 19.41 0.00 0.00 2.43
1625 2272 6.415573 AGTTCGCTGGTTTTCTAATCCTAAT 58.584 36.000 0.00 0.00 0.00 1.73
1650 2297 5.677567 CCATAGGGTTAAACAGGACGTATT 58.322 41.667 0.00 0.00 0.00 1.89
1653 2300 5.231702 AGGGTTAAACAGGACGTATTTCA 57.768 39.130 0.00 0.00 0.00 2.69
1661 2308 4.253685 ACAGGACGTATTTCACTCCAATG 58.746 43.478 0.00 0.00 30.84 2.82
1668 2315 6.578944 ACGTATTTCACTCCAATGCTATGTA 58.421 36.000 0.00 0.00 0.00 2.29
1679 2326 8.934697 ACTCCAATGCTATGTATTTTAGTCCTA 58.065 33.333 0.00 0.00 0.00 2.94
1762 2426 2.035632 TGCCGTTGTTTCCCAGAAAAT 58.964 42.857 0.00 0.00 0.00 1.82
1763 2427 2.432510 TGCCGTTGTTTCCCAGAAAATT 59.567 40.909 0.00 0.00 0.00 1.82
1799 2477 1.187567 GCAAGGTCCCCAACAATGCT 61.188 55.000 0.00 0.00 37.76 3.79
1800 2478 0.604578 CAAGGTCCCCAACAATGCTG 59.395 55.000 0.00 0.00 0.00 4.41
1801 2479 1.187567 AAGGTCCCCAACAATGCTGC 61.188 55.000 0.00 0.00 0.00 5.25
1802 2480 1.607467 GGTCCCCAACAATGCTGCT 60.607 57.895 0.00 0.00 0.00 4.24
1803 2481 1.187567 GGTCCCCAACAATGCTGCTT 61.188 55.000 0.00 0.00 0.00 3.91
1804 2482 0.244721 GTCCCCAACAATGCTGCTTC 59.755 55.000 0.00 0.00 0.00 3.86
1805 2483 0.178967 TCCCCAACAATGCTGCTTCA 60.179 50.000 0.00 0.00 0.00 3.02
1806 2484 0.037975 CCCCAACAATGCTGCTTCAC 60.038 55.000 0.00 0.00 0.00 3.18
1807 2485 0.675083 CCCAACAATGCTGCTTCACA 59.325 50.000 0.00 0.00 0.00 3.58
1808 2486 1.603678 CCCAACAATGCTGCTTCACAC 60.604 52.381 0.00 0.00 0.00 3.82
1809 2487 1.067364 CCAACAATGCTGCTTCACACA 59.933 47.619 0.00 0.00 0.00 3.72
1810 2488 2.121786 CAACAATGCTGCTTCACACAC 58.878 47.619 0.00 0.00 0.00 3.82
1811 2489 0.670162 ACAATGCTGCTTCACACACC 59.330 50.000 0.00 0.00 0.00 4.16
1868 2546 9.778741 TGTGAAGATCCTATCGCTAATAATTTT 57.221 29.630 0.00 0.00 0.00 1.82
1875 2553 8.958119 TCCTATCGCTAATAATTTTGACAACT 57.042 30.769 0.00 0.00 0.00 3.16
1885 2563 7.693969 ATAATTTTGACAACTTCAGGAGAGG 57.306 36.000 0.00 0.00 34.94 3.69
2046 2729 5.667626 AGGGATTACATACATGACTGGACTT 59.332 40.000 0.00 0.00 0.00 3.01
2136 2819 3.728718 CACTTGGCACATTGTTAACGAAC 59.271 43.478 0.00 0.00 39.30 3.95
2158 2850 0.179092 GATTAACACTAGCCGCCGGT 60.179 55.000 4.45 0.00 0.00 5.28
2283 3009 4.961511 AGCGCTGCGACGACCAAA 62.962 61.111 28.07 0.00 34.06 3.28
2354 3080 2.209064 GAACGTCTGCCCGCAGTCTA 62.209 60.000 15.93 0.00 43.96 2.59
2410 3136 1.478510 ACTCTTATGTGCTCGGTCTGG 59.521 52.381 0.00 0.00 0.00 3.86
2611 3337 1.165270 TGTCGCAGAAGTCGATCTCA 58.835 50.000 0.00 0.00 39.69 3.27
2701 3427 4.441695 TGCTCTGCCGGCTCTTCG 62.442 66.667 29.70 12.38 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 61 3.005791 AGGCTTTGTTGGTTACTGAATGC 59.994 43.478 0.00 0.00 0.00 3.56
507 651 0.184692 TGAGTGCCATGGACACCAAA 59.815 50.000 25.98 14.74 38.87 3.28
545 689 6.493115 TCCCTAGCATTCTTTGATCTCTCTAG 59.507 42.308 0.00 0.00 0.00 2.43
560 704 3.157881 TCTCGATCGATTCCCTAGCATT 58.842 45.455 19.78 0.00 0.00 3.56
576 735 1.982660 ATATCCGCACCTCTTCTCGA 58.017 50.000 0.00 0.00 0.00 4.04
586 745 1.009222 GCAGCAGCAATATCCGCAC 60.009 57.895 0.00 0.00 41.58 5.34
589 748 2.941333 CCGCAGCAGCAATATCCG 59.059 61.111 0.82 0.00 42.27 4.18
596 755 4.862447 CCCATAGCCGCAGCAGCA 62.862 66.667 2.79 0.00 43.56 4.41
607 766 4.609018 CTCGCCGCCACCCCATAG 62.609 72.222 0.00 0.00 0.00 2.23
616 775 2.083835 TATAACTCCAGCTCGCCGCC 62.084 60.000 0.00 0.00 40.39 6.13
654 813 1.135859 CGCGCTTTCTTCTCAAGCAAT 60.136 47.619 5.56 0.00 46.01 3.56
658 817 1.225583 CGCGCGCTTTCTTCTCAAG 60.226 57.895 30.48 4.48 0.00 3.02
659 818 2.667318 CCGCGCGCTTTCTTCTCAA 61.667 57.895 30.48 0.00 0.00 3.02
660 819 3.112075 CCGCGCGCTTTCTTCTCA 61.112 61.111 30.48 0.00 0.00 3.27
706 865 3.844090 GGGAGCTGCTCGTCCTCC 61.844 72.222 22.25 13.91 43.48 4.30
724 883 1.305201 TCTCAAGTGCAAACGGGAAC 58.695 50.000 0.00 0.00 0.00 3.62
727 886 1.879380 TCAATCTCAAGTGCAAACGGG 59.121 47.619 0.00 0.00 0.00 5.28
745 904 8.800332 TCTGATGATCGAATGAAGATAATCTCA 58.200 33.333 0.00 0.00 37.05 3.27
746 905 9.636879 TTCTGATGATCGAATGAAGATAATCTC 57.363 33.333 0.00 0.00 37.05 2.75
751 910 9.822185 TTCTTTTCTGATGATCGAATGAAGATA 57.178 29.630 11.29 5.04 0.00 1.98
760 919 7.148738 CGAACTCTTTTCTTTTCTGATGATCGA 60.149 37.037 0.00 0.00 0.00 3.59
763 922 7.736447 ACGAACTCTTTTCTTTTCTGATGAT 57.264 32.000 0.00 0.00 0.00 2.45
764 923 7.553881 AACGAACTCTTTTCTTTTCTGATGA 57.446 32.000 0.00 0.00 0.00 2.92
765 924 8.125448 AGAAACGAACTCTTTTCTTTTCTGATG 58.875 33.333 14.30 0.00 41.98 3.07
790 949 3.367087 CCACACGAGGAAGTACCACTTAG 60.367 52.174 0.00 0.00 38.80 2.18
793 952 0.966920 CCACACGAGGAAGTACCACT 59.033 55.000 0.00 0.00 42.04 4.00
794 953 0.677842 ACCACACGAGGAAGTACCAC 59.322 55.000 0.00 0.00 42.04 4.16
795 954 1.416243 AACCACACGAGGAAGTACCA 58.584 50.000 0.00 0.00 42.04 3.25
796 955 3.665745 TTAACCACACGAGGAAGTACC 57.334 47.619 0.00 0.00 39.35 3.34
797 956 5.467735 ACAAATTAACCACACGAGGAAGTAC 59.532 40.000 0.00 0.00 0.00 2.73
837 1018 7.386848 CGTTGTTAACCTCTTCTTCTTGGATAA 59.613 37.037 2.48 0.00 0.00 1.75
841 1022 4.213482 CCGTTGTTAACCTCTTCTTCTTGG 59.787 45.833 2.48 0.00 0.00 3.61
842 1023 4.213482 CCCGTTGTTAACCTCTTCTTCTTG 59.787 45.833 2.48 0.00 0.00 3.02
843 1024 4.102054 TCCCGTTGTTAACCTCTTCTTCTT 59.898 41.667 2.48 0.00 0.00 2.52
844 1025 3.644738 TCCCGTTGTTAACCTCTTCTTCT 59.355 43.478 2.48 0.00 0.00 2.85
845 1026 3.744942 GTCCCGTTGTTAACCTCTTCTTC 59.255 47.826 2.48 0.00 0.00 2.87
850 1031 0.320160 GCGTCCCGTTGTTAACCTCT 60.320 55.000 2.48 0.00 0.00 3.69
857 1038 0.106149 AAAGAGAGCGTCCCGTTGTT 59.894 50.000 0.00 0.00 0.00 2.83
945 1141 4.423209 GCAGGGGAGGGGAGGTCT 62.423 72.222 0.00 0.00 0.00 3.85
947 1143 1.990370 ATATGCAGGGGAGGGGAGGT 61.990 60.000 0.00 0.00 0.00 3.85
949 1145 1.912043 CTTATATGCAGGGGAGGGGAG 59.088 57.143 0.00 0.00 0.00 4.30
950 1146 1.225694 ACTTATATGCAGGGGAGGGGA 59.774 52.381 0.00 0.00 0.00 4.81
951 1147 1.747444 ACTTATATGCAGGGGAGGGG 58.253 55.000 0.00 0.00 0.00 4.79
952 1148 2.840651 CCTACTTATATGCAGGGGAGGG 59.159 54.545 0.00 0.00 0.00 4.30
985 1181 1.457455 CTTTGGTGGCCAGGGTTGT 60.457 57.895 5.11 0.00 33.81 3.32
986 1182 2.871253 GCTTTGGTGGCCAGGGTTG 61.871 63.158 5.11 0.00 33.81 3.77
987 1183 2.524148 GCTTTGGTGGCCAGGGTT 60.524 61.111 5.11 0.00 33.81 4.11
988 1184 3.387609 TTGCTTTGGTGGCCAGGGT 62.388 57.895 5.11 0.00 33.81 4.34
1012 1208 1.687494 GACGATGTCGCTGGTTCTGC 61.687 60.000 1.77 0.00 44.43 4.26
1014 1210 4.891566 GACGATGTCGCTGGTTCT 57.108 55.556 1.77 0.00 44.43 3.01
1064 1261 1.452108 CCATCAGGTCCCGAAAGCC 60.452 63.158 0.00 0.00 0.00 4.35
1114 1344 3.997064 CTCCTTCTCCGGCACTGCG 62.997 68.421 0.00 0.00 0.00 5.18
1260 1493 2.590092 GGTCGGGGAACATGGAGG 59.410 66.667 0.00 0.00 0.00 4.30
1271 1504 3.489513 GAAGGGGATGGGGTCGGG 61.490 72.222 0.00 0.00 0.00 5.14
1431 1679 3.513680 AAAAACAAGACCGAACCAACC 57.486 42.857 0.00 0.00 0.00 3.77
1439 1687 5.494632 AACCAGAACTAAAAACAAGACCG 57.505 39.130 0.00 0.00 0.00 4.79
1532 1795 8.596271 TTGTTCGACATAATCACTTGACTAAA 57.404 30.769 0.00 0.00 0.00 1.85
1599 2246 5.420409 AGGATTAGAAAACCAGCGAACTAG 58.580 41.667 0.00 0.00 0.00 2.57
1602 2249 6.487103 CATTAGGATTAGAAAACCAGCGAAC 58.513 40.000 0.00 0.00 0.00 3.95
1625 2272 2.355310 CGTCCTGTTTAACCCTATGGCA 60.355 50.000 0.00 0.00 33.59 4.92
1650 2297 9.109393 GACTAAAATACATAGCATTGGAGTGAA 57.891 33.333 0.00 0.00 0.00 3.18
1653 2300 7.806180 AGGACTAAAATACATAGCATTGGAGT 58.194 34.615 0.00 0.00 0.00 3.85
1661 2308 8.446599 TTGCCTTTAGGACTAAAATACATAGC 57.553 34.615 0.00 2.58 34.95 2.97
1668 2315 5.775195 ACTGCTTTGCCTTTAGGACTAAAAT 59.225 36.000 0.00 0.00 34.95 1.82
1679 2326 4.588528 TGGATTCTTTACTGCTTTGCCTTT 59.411 37.500 0.00 0.00 0.00 3.11
1746 2410 5.989168 CCTACCAAATTTTCTGGGAAACAAC 59.011 40.000 0.00 0.00 38.36 3.32
1762 2426 0.607620 GCAATTGCAGGCCTACCAAA 59.392 50.000 25.36 6.58 41.59 3.28
1763 2427 2.275880 GCAATTGCAGGCCTACCAA 58.724 52.632 25.36 17.44 41.59 3.67
1799 2477 1.203523 GGTTTTGTGGTGTGTGAAGCA 59.796 47.619 0.00 0.00 0.00 3.91
1800 2478 1.203523 TGGTTTTGTGGTGTGTGAAGC 59.796 47.619 0.00 0.00 0.00 3.86
1801 2479 3.584406 TTGGTTTTGTGGTGTGTGAAG 57.416 42.857 0.00 0.00 0.00 3.02
1802 2480 4.543590 ATTTGGTTTTGTGGTGTGTGAA 57.456 36.364 0.00 0.00 0.00 3.18
1803 2481 4.142138 GGTATTTGGTTTTGTGGTGTGTGA 60.142 41.667 0.00 0.00 0.00 3.58
1804 2482 4.116238 GGTATTTGGTTTTGTGGTGTGTG 58.884 43.478 0.00 0.00 0.00 3.82
1805 2483 3.769844 TGGTATTTGGTTTTGTGGTGTGT 59.230 39.130 0.00 0.00 0.00 3.72
1806 2484 4.392921 TGGTATTTGGTTTTGTGGTGTG 57.607 40.909 0.00 0.00 0.00 3.82
1807 2485 5.179533 GTTTGGTATTTGGTTTTGTGGTGT 58.820 37.500 0.00 0.00 0.00 4.16
1808 2486 4.572795 GGTTTGGTATTTGGTTTTGTGGTG 59.427 41.667 0.00 0.00 0.00 4.17
1809 2487 4.225267 TGGTTTGGTATTTGGTTTTGTGGT 59.775 37.500 0.00 0.00 0.00 4.16
1810 2488 4.572795 GTGGTTTGGTATTTGGTTTTGTGG 59.427 41.667 0.00 0.00 0.00 4.17
1811 2489 5.423886 AGTGGTTTGGTATTTGGTTTTGTG 58.576 37.500 0.00 0.00 0.00 3.33
1868 2546 4.771114 TTTTCCTCTCCTGAAGTTGTCA 57.229 40.909 0.00 0.00 34.17 3.58
1895 2573 1.647084 GTTCGTTCGTTTGCTGCCT 59.353 52.632 0.00 0.00 0.00 4.75
1897 2575 0.657368 CTGGTTCGTTCGTTTGCTGC 60.657 55.000 0.00 0.00 0.00 5.25
1898 2576 0.934496 TCTGGTTCGTTCGTTTGCTG 59.066 50.000 0.00 0.00 0.00 4.41
2020 2703 6.158695 AGTCCAGTCATGTATGTAATCCCTTT 59.841 38.462 0.00 0.00 0.00 3.11
2046 2729 4.072131 CCCTTCATTCTTTTTCTCCGTCA 58.928 43.478 0.00 0.00 0.00 4.35
2136 2819 0.878961 GGCGGCTAGTGTTAATCCCG 60.879 60.000 0.00 0.00 38.76 5.14
2158 2850 5.005971 GCAGCTCACGTATTTAATTAACCGA 59.994 40.000 14.52 0.00 0.00 4.69
2283 3009 5.723887 AGGAGGAAGTTCAATCACTACTGAT 59.276 40.000 5.01 0.00 38.94 2.90
2530 3256 1.212751 CATCTGCACCGACGAGTCA 59.787 57.895 0.00 0.00 0.00 3.41
2576 3302 2.262211 CGACATGACATTCGAGAGCAA 58.738 47.619 0.00 0.00 37.43 3.91
2611 3337 3.394606 AGGTGGTGGAGTTATTTCAGTGT 59.605 43.478 0.00 0.00 0.00 3.55
2665 3391 2.801342 GCAGATTGAAACCGCAAAACCA 60.801 45.455 0.00 0.00 0.00 3.67
2701 3427 2.973945 AGGACGAAACCTGCAGTAATC 58.026 47.619 13.81 6.40 39.01 1.75


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

AutoCloner maintained by Alex Coulton.