Multiple sequence alignment - TraesCS1D01G322200

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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 TraesCS1D01G322200 chr1D 100.000 2903 0 0 1 2903 415298482 415301384 0.000000e+00 5361.0
1 TraesCS1D01G322200 chr1D 78.907 915 139 25 1003 1881 415322942 415323838 3.250000e-159 571.0
2 TraesCS1D01G322200 chr1D 84.559 136 18 1 1742 1874 89230549 89230684 6.530000e-27 132.0
3 TraesCS1D01G322200 chr1B 93.006 1244 47 8 688 1919 561543931 561545146 0.000000e+00 1779.0
4 TraesCS1D01G322200 chr1B 88.526 1316 87 36 609 1895 561551405 561552685 0.000000e+00 1535.0
5 TraesCS1D01G322200 chr1B 91.867 664 41 6 2 658 561543273 561543930 0.000000e+00 915.0
6 TraesCS1D01G322200 chr1B 89.819 442 32 8 1922 2355 561545191 561545627 3.270000e-154 555.0
7 TraesCS1D01G322200 chr1B 92.553 376 20 4 2534 2903 561553785 561554158 1.530000e-147 532.0
8 TraesCS1D01G322200 chr1B 77.805 829 132 28 1111 1904 563121535 563120724 5.670000e-127 464.0
9 TraesCS1D01G322200 chr1B 81.547 569 77 15 2 560 561550656 561551206 7.380000e-121 444.0
10 TraesCS1D01G322200 chr1B 93.388 242 12 3 2273 2514 561553344 561553581 3.560000e-94 355.0
11 TraesCS1D01G322200 chr1B 85.864 191 12 6 1922 2108 561552790 561552969 3.820000e-44 189.0
12 TraesCS1D01G322200 chr1B 82.353 136 21 1 1742 1874 142510373 142510508 6.570000e-22 115.0
13 TraesCS1D01G322200 chr1B 82.443 131 20 1 2240 2367 561554296 561554426 8.500000e-21 111.0
14 TraesCS1D01G322200 chr1A 91.422 1224 48 10 688 1904 512665350 512666523 0.000000e+00 1626.0
15 TraesCS1D01G322200 chr1A 92.044 729 39 9 2115 2841 512666751 512667462 0.000000e+00 1007.0
16 TraesCS1D01G322200 chr1A 92.436 661 44 4 3 658 512664690 512665349 0.000000e+00 939.0
17 TraesCS1D01G322200 chr1A 78.912 441 67 12 1486 1904 513840556 513840120 2.850000e-70 276.0
18 TraesCS1D01G322200 chr7D 75.862 174 33 8 1241 1411 553370510 553370677 2.400000e-11 80.5


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 TraesCS1D01G322200 chr1D 415298482 415301384 2902 False 5361.000000 5361 100.000000 1 2903 1 chr1D.!!$F2 2902
1 TraesCS1D01G322200 chr1D 415322942 415323838 896 False 571.000000 571 78.907000 1003 1881 1 chr1D.!!$F3 878
2 TraesCS1D01G322200 chr1B 561543273 561545627 2354 False 1083.000000 1779 91.564000 2 2355 3 chr1B.!!$F2 2353
3 TraesCS1D01G322200 chr1B 561550656 561554426 3770 False 527.666667 1535 87.386833 2 2903 6 chr1B.!!$F3 2901
4 TraesCS1D01G322200 chr1B 563120724 563121535 811 True 464.000000 464 77.805000 1111 1904 1 chr1B.!!$R1 793
5 TraesCS1D01G322200 chr1A 512664690 512667462 2772 False 1190.666667 1626 91.967333 3 2841 3 chr1A.!!$F1 2838

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
96 97 1.269448 CCACCAACATTAAGCAAGCGT 59.731 47.619 0.00 0.0 0.0 5.07 F
675 874 1.600023 TTCGGACGAAAAATGCACCT 58.400 45.000 4.47 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1499 1.630369 AGCACCAAGATCTGCTTACCA 59.370 47.619 0.0 0.0 41.04 3.25 R
2131 2572 0.737219 GCTCCTTGCATCATCACCAC 59.263 55.000 0.0 0.0 42.31 4.16 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
30 31 7.548075 TCATTCTTTACGTGACCTTTAATCTCC 59.452 37.037 0.00 0.00 0.00 3.71
59 60 4.771054 GGAACCCAAGTCTCAGTCTACTTA 59.229 45.833 0.00 0.00 34.23 2.24
67 68 7.378966 CAAGTCTCAGTCTACTTATGAAACCA 58.621 38.462 0.00 0.00 34.23 3.67
71 72 4.525487 TCAGTCTACTTATGAAACCACCGT 59.475 41.667 0.00 0.00 0.00 4.83
96 97 1.269448 CCACCAACATTAAGCAAGCGT 59.731 47.619 0.00 0.00 0.00 5.07
142 143 6.932051 TCTTTGAAATGAAAACGAATTGCAC 58.068 32.000 0.00 0.00 25.93 4.57
200 201 6.505048 AGTACCACAAAAAGTACTTAGGGT 57.495 37.500 8.92 13.60 45.30 4.34
304 310 6.589139 GTGTAGTACTATGGTTTGTTGACCTC 59.411 42.308 5.75 0.00 40.47 3.85
450 459 1.755959 TGGGATGGAATGCGGAAATTG 59.244 47.619 0.00 0.00 34.31 2.32
459 468 4.834892 CGGAAATTGCAGCCCGCG 62.835 66.667 0.00 0.00 46.97 6.46
479 488 2.592287 GTTTTGGTCGGGTGCGGA 60.592 61.111 0.00 0.00 0.00 5.54
533 548 4.908736 AGCATTATGTGAAATGTGTACGC 58.091 39.130 0.00 0.00 38.78 4.42
575 752 5.403246 ACTATGCCGCGATAAGATCTAAAG 58.597 41.667 8.23 0.00 0.00 1.85
616 794 7.753309 TTAAAGGACGGAGATTTTTCATTGA 57.247 32.000 0.00 0.00 0.00 2.57
668 867 5.502153 TTGGAAAGAATTCGGACGAAAAA 57.498 34.783 11.41 0.00 37.69 1.94
669 868 5.699097 TGGAAAGAATTCGGACGAAAAAT 57.301 34.783 11.41 1.19 37.69 1.82
670 869 5.457140 TGGAAAGAATTCGGACGAAAAATG 58.543 37.500 11.41 0.00 37.69 2.32
671 870 4.323602 GGAAAGAATTCGGACGAAAAATGC 59.676 41.667 11.41 0.00 37.69 3.56
672 871 4.497473 AAGAATTCGGACGAAAAATGCA 57.503 36.364 11.41 0.00 37.69 3.96
673 872 3.821841 AGAATTCGGACGAAAAATGCAC 58.178 40.909 11.41 0.00 37.69 4.57
674 873 2.629639 ATTCGGACGAAAAATGCACC 57.370 45.000 11.41 0.00 37.69 5.01
675 874 1.600023 TTCGGACGAAAAATGCACCT 58.400 45.000 4.47 0.00 0.00 4.00
676 875 1.600023 TCGGACGAAAAATGCACCTT 58.400 45.000 0.00 0.00 0.00 3.50
677 876 2.768698 TCGGACGAAAAATGCACCTTA 58.231 42.857 0.00 0.00 0.00 2.69
678 877 2.481185 TCGGACGAAAAATGCACCTTAC 59.519 45.455 0.00 0.00 0.00 2.34
679 878 2.413634 CGGACGAAAAATGCACCTTACC 60.414 50.000 0.00 0.00 0.00 2.85
680 879 2.094906 GGACGAAAAATGCACCTTACCC 60.095 50.000 0.00 0.00 0.00 3.69
681 880 2.554893 GACGAAAAATGCACCTTACCCA 59.445 45.455 0.00 0.00 0.00 4.51
682 881 2.959707 ACGAAAAATGCACCTTACCCAA 59.040 40.909 0.00 0.00 0.00 4.12
683 882 3.576550 ACGAAAAATGCACCTTACCCAAT 59.423 39.130 0.00 0.00 0.00 3.16
684 883 4.039852 ACGAAAAATGCACCTTACCCAATT 59.960 37.500 0.00 0.00 0.00 2.32
685 884 5.244178 ACGAAAAATGCACCTTACCCAATTA 59.756 36.000 0.00 0.00 0.00 1.40
686 885 5.575218 CGAAAAATGCACCTTACCCAATTAC 59.425 40.000 0.00 0.00 0.00 1.89
740 941 6.183360 GCTGTACTGGTAATTAAGCACTTCTG 60.183 42.308 1.65 0.00 0.00 3.02
743 944 4.009675 CTGGTAATTAAGCACTTCTGCCA 58.990 43.478 0.00 0.00 45.53 4.92
744 945 4.599041 TGGTAATTAAGCACTTCTGCCAT 58.401 39.130 0.00 0.00 45.53 4.40
746 947 5.480073 TGGTAATTAAGCACTTCTGCCATTT 59.520 36.000 0.00 0.00 45.53 2.32
747 948 6.014669 TGGTAATTAAGCACTTCTGCCATTTT 60.015 34.615 0.00 0.00 45.53 1.82
748 949 6.311200 GGTAATTAAGCACTTCTGCCATTTTG 59.689 38.462 0.00 0.00 45.53 2.44
749 950 2.825861 AAGCACTTCTGCCATTTTGG 57.174 45.000 0.00 0.00 45.53 3.28
750 951 1.708341 AGCACTTCTGCCATTTTGGT 58.292 45.000 0.00 0.00 45.53 3.67
754 961 3.002553 GCACTTCTGCCATTTTGGTTTTG 59.997 43.478 0.00 0.00 40.46 2.44
778 985 7.100409 TGGTTTTGGTTTTGGTTTCTTTCTAG 58.900 34.615 0.00 0.00 0.00 2.43
779 986 7.101054 GGTTTTGGTTTTGGTTTCTTTCTAGT 58.899 34.615 0.00 0.00 0.00 2.57
780 987 8.252417 GGTTTTGGTTTTGGTTTCTTTCTAGTA 58.748 33.333 0.00 0.00 0.00 1.82
781 988 9.297586 GTTTTGGTTTTGGTTTCTTTCTAGTAG 57.702 33.333 0.00 0.00 0.00 2.57
782 989 8.584063 TTTGGTTTTGGTTTCTTTCTAGTAGT 57.416 30.769 0.00 0.00 0.00 2.73
783 990 9.683870 TTTGGTTTTGGTTTCTTTCTAGTAGTA 57.316 29.630 0.00 0.00 0.00 1.82
784 991 9.856162 TTGGTTTTGGTTTCTTTCTAGTAGTAT 57.144 29.630 0.00 0.00 0.00 2.12
887 1099 3.253188 TCACTTCCCGCTCTTTTGAATTG 59.747 43.478 0.00 0.00 0.00 2.32
888 1100 3.253188 CACTTCCCGCTCTTTTGAATTGA 59.747 43.478 0.00 0.00 0.00 2.57
889 1101 3.253432 ACTTCCCGCTCTTTTGAATTGAC 59.747 43.478 0.00 0.00 0.00 3.18
890 1102 1.804151 TCCCGCTCTTTTGAATTGACG 59.196 47.619 0.00 0.00 0.00 4.35
975 1229 2.264480 CGCCAGAACCCGATCACA 59.736 61.111 0.00 0.00 0.00 3.58
1236 1499 1.840635 GATAGCCAAGGACAAGGAGGT 59.159 52.381 0.00 0.00 0.00 3.85
1843 2154 1.004560 CTCGTGCAAGCCCTCAAGA 60.005 57.895 0.00 0.00 0.00 3.02
1895 2206 1.949847 CTGTCGGCTCCGGATGAACT 61.950 60.000 3.57 0.00 40.25 3.01
1919 2265 1.003580 CTAGGCCAAAGTCAGGAGCAA 59.996 52.381 5.01 0.00 0.00 3.91
1920 2266 0.538287 AGGCCAAAGTCAGGAGCAAC 60.538 55.000 5.01 0.00 0.00 4.17
1950 2342 5.372343 TTCATGGATTATATATGCCGGCT 57.628 39.130 29.70 15.76 0.00 5.52
1951 2343 6.493189 TTCATGGATTATATATGCCGGCTA 57.507 37.500 29.70 17.52 0.00 3.93
2064 2457 9.853177 AGATATTACTTGTAAGAAATTCCTGGG 57.147 33.333 0.00 0.00 0.00 4.45
2135 2576 9.893305 CGATTTTTCTTTTATTACTTCTGTGGT 57.107 29.630 0.00 0.00 0.00 4.16
2140 2581 9.567776 TTTCTTTTATTACTTCTGTGGTGATGA 57.432 29.630 0.00 0.00 0.00 2.92
2141 2582 9.739276 TTCTTTTATTACTTCTGTGGTGATGAT 57.261 29.630 0.00 0.00 0.00 2.45
2142 2583 9.166173 TCTTTTATTACTTCTGTGGTGATGATG 57.834 33.333 0.00 0.00 0.00 3.07
2143 2584 6.925610 TTATTACTTCTGTGGTGATGATGC 57.074 37.500 0.00 0.00 0.00 3.91
2144 2585 2.865119 ACTTCTGTGGTGATGATGCA 57.135 45.000 0.00 0.00 0.00 3.96
2145 2586 3.144657 ACTTCTGTGGTGATGATGCAA 57.855 42.857 0.00 0.00 0.00 4.08
2146 2587 3.079578 ACTTCTGTGGTGATGATGCAAG 58.920 45.455 0.00 0.00 0.00 4.01
2147 2588 2.118313 TCTGTGGTGATGATGCAAGG 57.882 50.000 0.00 0.00 0.00 3.61
2148 2589 1.629861 TCTGTGGTGATGATGCAAGGA 59.370 47.619 0.00 0.00 0.00 3.36
2149 2590 2.014857 CTGTGGTGATGATGCAAGGAG 58.985 52.381 0.00 0.00 0.00 3.69
2196 2637 6.150396 TCAAGTATAAGGAAGTAGCTCTGC 57.850 41.667 0.00 0.00 0.00 4.26
2211 2652 3.557595 AGCTCTGCATGAATAAACGCTAC 59.442 43.478 0.00 0.00 0.00 3.58
2261 2706 2.047061 AGCCTGTCAGTGTCACCTTAA 58.953 47.619 0.00 0.00 0.00 1.85
2302 3007 3.485394 TGATACACACAATGCACAACCT 58.515 40.909 0.00 0.00 0.00 3.50
2396 3101 4.729227 TGTGCCGTAAATCTGTATCAGA 57.271 40.909 1.92 1.92 44.99 3.27
2397 3102 4.682787 TGTGCCGTAAATCTGTATCAGAG 58.317 43.478 5.71 0.00 44.08 3.35
2478 3183 8.424918 AGAAATAACACTCGATATCCATGACTT 58.575 33.333 0.00 0.00 0.00 3.01
2479 3184 9.692749 GAAATAACACTCGATATCCATGACTTA 57.307 33.333 0.00 0.00 0.00 2.24
2535 3424 8.298854 TGATTTTCTTCCATACAACATGAACAG 58.701 33.333 0.00 0.00 0.00 3.16
2549 3438 1.142667 TGAACAGTGTGCCCATCTTCA 59.857 47.619 0.00 0.00 0.00 3.02
2558 3447 3.071312 TGTGCCCATCTTCAAAGCAAAAT 59.929 39.130 0.00 0.00 34.79 1.82
2588 3477 0.612732 ATCGAAGGTGGTCCGTGGTA 60.613 55.000 0.00 0.00 39.05 3.25
2616 3505 1.334054 CAATGTGCTTGAAGCTTCGC 58.666 50.000 21.11 18.70 42.97 4.70
2686 3575 9.855021 GTATGCAAAATGATACAACCTAACTTT 57.145 29.630 0.00 0.00 0.00 2.66
2747 3636 8.565896 TTAGCAATCATTCTAAACATGTGACT 57.434 30.769 0.00 0.00 0.00 3.41
2774 3665 5.387279 CGTAAAATACTTGCCATGAACGTT 58.613 37.500 0.00 0.00 0.00 3.99
2795 3687 9.651913 AACGTTTGCCATTTATATCTGATTTTT 57.348 25.926 0.00 0.00 0.00 1.94
2891 3788 5.954335 ACTCATGTTAACTGCAAATAAGGC 58.046 37.500 7.22 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.610248 TTAAAGGTCACGTAAAGAATGATTGA 57.390 30.769 0.00 0.00 0.00 2.57
8 9 5.404946 CGGAGATTAAAGGTCACGTAAAGA 58.595 41.667 0.00 0.00 0.00 2.52
30 31 0.036294 GAGACTTGGGTTCCCTTCCG 60.036 60.000 9.43 0.00 0.00 4.30
50 51 5.948162 TCTACGGTGGTTTCATAAGTAGACT 59.052 40.000 0.00 0.00 34.44 3.24
59 60 2.093128 GGTGGATCTACGGTGGTTTCAT 60.093 50.000 2.84 0.00 0.00 2.57
67 68 4.766375 CTTAATGTTGGTGGATCTACGGT 58.234 43.478 2.84 0.00 0.00 4.83
71 72 4.640201 GCTTGCTTAATGTTGGTGGATCTA 59.360 41.667 0.00 0.00 0.00 1.98
96 97 3.714798 AGAAGTTTGTGTAGGAAGGTGGA 59.285 43.478 0.00 0.00 0.00 4.02
142 143 1.540267 TTGGACCCAAAATAGTGCCG 58.460 50.000 0.00 0.00 32.44 5.69
200 201 1.340893 TGATCCTGGTACGGTTCCGTA 60.341 52.381 18.34 18.34 42.88 4.02
533 548 2.289547 AGTCAAACCGGTTTCATCAACG 59.710 45.455 29.48 16.32 36.05 4.10
575 752 7.413767 CGTCCTTTAATAACTCCTAAAACAGGC 60.414 40.741 0.00 0.00 45.10 4.85
631 809 3.401033 TTCCAAGAGATGCGACTTTCA 57.599 42.857 0.00 0.00 0.00 2.69
658 857 2.413634 GGTAAGGTGCATTTTTCGTCCG 60.414 50.000 0.00 0.00 0.00 4.79
659 858 2.094906 GGGTAAGGTGCATTTTTCGTCC 60.095 50.000 0.00 0.00 0.00 4.79
660 859 2.554893 TGGGTAAGGTGCATTTTTCGTC 59.445 45.455 0.00 0.00 0.00 4.20
661 860 2.588620 TGGGTAAGGTGCATTTTTCGT 58.411 42.857 0.00 0.00 0.00 3.85
662 861 3.651803 TTGGGTAAGGTGCATTTTTCG 57.348 42.857 0.00 0.00 0.00 3.46
663 862 5.575218 CGTAATTGGGTAAGGTGCATTTTTC 59.425 40.000 0.00 0.00 0.00 2.29
664 863 5.244178 TCGTAATTGGGTAAGGTGCATTTTT 59.756 36.000 0.00 0.00 0.00 1.94
665 864 4.767928 TCGTAATTGGGTAAGGTGCATTTT 59.232 37.500 0.00 0.00 0.00 1.82
666 865 4.337145 TCGTAATTGGGTAAGGTGCATTT 58.663 39.130 0.00 0.00 0.00 2.32
667 866 3.958018 TCGTAATTGGGTAAGGTGCATT 58.042 40.909 0.00 0.00 0.00 3.56
668 867 3.637911 TCGTAATTGGGTAAGGTGCAT 57.362 42.857 0.00 0.00 0.00 3.96
669 868 3.420300 TTCGTAATTGGGTAAGGTGCA 57.580 42.857 0.00 0.00 0.00 4.57
670 869 3.128068 CCTTTCGTAATTGGGTAAGGTGC 59.872 47.826 7.42 0.00 0.00 5.01
671 870 4.581868 TCCTTTCGTAATTGGGTAAGGTG 58.418 43.478 12.48 0.00 34.98 4.00
672 871 4.914177 TCCTTTCGTAATTGGGTAAGGT 57.086 40.909 12.48 0.00 34.98 3.50
673 872 5.941647 TCTTTCCTTTCGTAATTGGGTAAGG 59.058 40.000 8.67 8.67 34.77 2.69
674 873 7.625828 ATCTTTCCTTTCGTAATTGGGTAAG 57.374 36.000 0.00 0.00 0.00 2.34
675 874 9.689501 ATTATCTTTCCTTTCGTAATTGGGTAA 57.310 29.630 0.00 0.00 0.00 2.85
677 876 9.689501 TTATTATCTTTCCTTTCGTAATTGGGT 57.310 29.630 0.00 0.00 0.00 4.51
685 884 8.762426 GCTCGTATTTATTATCTTTCCTTTCGT 58.238 33.333 0.00 0.00 0.00 3.85
686 885 8.979574 AGCTCGTATTTATTATCTTTCCTTTCG 58.020 33.333 0.00 0.00 0.00 3.46
740 941 3.445450 ACCAAAACCAAAACCAAAATGGC 59.555 39.130 0.00 0.00 42.67 4.40
743 944 6.042093 ACCAAAACCAAAACCAAAACCAAAAT 59.958 30.769 0.00 0.00 0.00 1.82
744 945 5.362717 ACCAAAACCAAAACCAAAACCAAAA 59.637 32.000 0.00 0.00 0.00 2.44
746 947 4.470602 ACCAAAACCAAAACCAAAACCAA 58.529 34.783 0.00 0.00 0.00 3.67
747 948 4.100279 ACCAAAACCAAAACCAAAACCA 57.900 36.364 0.00 0.00 0.00 3.67
748 949 5.241949 AGAAACCAAAACCAAAACCAAAACC 59.758 36.000 0.00 0.00 0.00 3.27
749 950 6.320494 AGAAACCAAAACCAAAACCAAAAC 57.680 33.333 0.00 0.00 0.00 2.43
750 951 6.961360 AAGAAACCAAAACCAAAACCAAAA 57.039 29.167 0.00 0.00 0.00 2.44
754 961 7.101054 ACTAGAAAGAAACCAAAACCAAAACC 58.899 34.615 0.00 0.00 0.00 3.27
784 991 9.607988 TCGGATAGTATTAATGCAAGAGAAAAA 57.392 29.630 6.31 0.00 0.00 1.94
975 1229 2.910479 TCAGCACCGTCGTGGACT 60.910 61.111 3.47 0.00 42.00 3.85
1107 1364 2.757077 CCAAGGAACCGCCCTTCT 59.243 61.111 0.00 0.00 44.30 2.85
1197 1460 2.430921 GCGGCCGGTAGATCATCG 60.431 66.667 29.38 0.00 0.00 3.84
1236 1499 1.630369 AGCACCAAGATCTGCTTACCA 59.370 47.619 0.00 0.00 41.04 3.25
1895 2206 3.366396 CTCCTGACTTTGGCCTAGACTA 58.634 50.000 3.32 0.00 0.00 2.59
1919 2265 9.624373 GCATATATAATCCATGAATCTGAAGGT 57.376 33.333 0.00 0.00 0.00 3.50
1920 2266 9.064706 GGCATATATAATCCATGAATCTGAAGG 57.935 37.037 0.00 0.00 0.00 3.46
1951 2343 7.706607 GCAATCCTTTTAAAACAGAACAGAACT 59.293 33.333 0.00 0.00 0.00 3.01
2064 2457 8.385111 CAACATGCATTTCTCCATTGATTAAAC 58.615 33.333 0.00 0.00 0.00 2.01
2109 2550 9.893305 ACCACAGAAGTAATAAAAGAAAAATCG 57.107 29.630 0.00 0.00 0.00 3.34
2114 2555 9.567776 TCATCACCACAGAAGTAATAAAAGAAA 57.432 29.630 0.00 0.00 0.00 2.52
2115 2556 9.739276 ATCATCACCACAGAAGTAATAAAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
2116 2557 9.166173 CATCATCACCACAGAAGTAATAAAAGA 57.834 33.333 0.00 0.00 0.00 2.52
2117 2558 7.912250 GCATCATCACCACAGAAGTAATAAAAG 59.088 37.037 0.00 0.00 0.00 2.27
2118 2559 7.392953 TGCATCATCACCACAGAAGTAATAAAA 59.607 33.333 0.00 0.00 0.00 1.52
2119 2560 6.883756 TGCATCATCACCACAGAAGTAATAAA 59.116 34.615 0.00 0.00 0.00 1.40
2120 2561 6.413892 TGCATCATCACCACAGAAGTAATAA 58.586 36.000 0.00 0.00 0.00 1.40
2121 2562 5.988287 TGCATCATCACCACAGAAGTAATA 58.012 37.500 0.00 0.00 0.00 0.98
2122 2563 4.847198 TGCATCATCACCACAGAAGTAAT 58.153 39.130 0.00 0.00 0.00 1.89
2123 2564 4.284829 TGCATCATCACCACAGAAGTAA 57.715 40.909 0.00 0.00 0.00 2.24
2124 2565 3.979101 TGCATCATCACCACAGAAGTA 57.021 42.857 0.00 0.00 0.00 2.24
2125 2566 2.865119 TGCATCATCACCACAGAAGT 57.135 45.000 0.00 0.00 0.00 3.01
2126 2567 2.422479 CCTTGCATCATCACCACAGAAG 59.578 50.000 0.00 0.00 0.00 2.85
2127 2568 2.040145 TCCTTGCATCATCACCACAGAA 59.960 45.455 0.00 0.00 0.00 3.02
2128 2569 1.629861 TCCTTGCATCATCACCACAGA 59.370 47.619 0.00 0.00 0.00 3.41
2129 2570 2.014857 CTCCTTGCATCATCACCACAG 58.985 52.381 0.00 0.00 0.00 3.66
2130 2571 1.951895 GCTCCTTGCATCATCACCACA 60.952 52.381 0.00 0.00 42.31 4.17
2131 2572 0.737219 GCTCCTTGCATCATCACCAC 59.263 55.000 0.00 0.00 42.31 4.16
2132 2573 3.179925 GCTCCTTGCATCATCACCA 57.820 52.632 0.00 0.00 42.31 4.17
2143 2584 3.057033 ACTTAAAGCTGCAATGCTCCTTG 60.057 43.478 6.82 0.61 43.24 3.61
2144 2585 3.160269 ACTTAAAGCTGCAATGCTCCTT 58.840 40.909 6.82 5.97 43.24 3.36
2145 2586 2.800250 ACTTAAAGCTGCAATGCTCCT 58.200 42.857 6.82 0.00 43.24 3.69
2146 2587 3.582714 AACTTAAAGCTGCAATGCTCC 57.417 42.857 6.82 0.00 43.24 4.70
2147 2588 5.920273 TGTAAAACTTAAAGCTGCAATGCTC 59.080 36.000 6.82 0.00 43.24 4.26
2148 2589 5.691754 GTGTAAAACTTAAAGCTGCAATGCT 59.308 36.000 6.82 0.00 46.40 3.79
2149 2590 5.691754 AGTGTAAAACTTAAAGCTGCAATGC 59.308 36.000 1.02 0.00 34.57 3.56
2184 2625 5.732288 CGTTTATTCATGCAGAGCTACTTC 58.268 41.667 0.00 0.00 0.00 3.01
2196 2637 6.292381 GCTGAACTAGGTAGCGTTTATTCATG 60.292 42.308 0.00 0.00 0.00 3.07
2211 2652 1.226717 GCTCGACCGCTGAACTAGG 60.227 63.158 0.00 0.00 0.00 3.02
2261 2706 8.955388 TGTATCAGTGTATGTAATGTTGCAAAT 58.045 29.630 0.00 0.00 0.00 2.32
2302 3007 2.571212 CAGGGCTGCAAATATACCGAA 58.429 47.619 0.50 0.00 0.00 4.30
2346 3051 5.148651 AGATTAACGGGGCTGTATATGTC 57.851 43.478 0.00 0.00 0.00 3.06
2396 3101 3.650139 ACTTGCGTCTTGTAACGATTCT 58.350 40.909 0.00 0.00 45.37 2.40
2397 3102 3.479866 CGACTTGCGTCTTGTAACGATTC 60.480 47.826 0.00 0.00 45.37 2.52
2478 3183 6.040504 ACAGTTGTAGACATCGAGGCATAATA 59.959 38.462 0.00 0.00 0.00 0.98
2479 3184 5.163405 ACAGTTGTAGACATCGAGGCATAAT 60.163 40.000 0.00 0.00 0.00 1.28
2480 3185 4.159693 ACAGTTGTAGACATCGAGGCATAA 59.840 41.667 0.00 0.00 0.00 1.90
2483 3188 1.893137 ACAGTTGTAGACATCGAGGCA 59.107 47.619 0.00 0.00 0.00 4.75
2535 3424 0.961019 TGCTTTGAAGATGGGCACAC 59.039 50.000 0.00 0.00 0.00 3.82
2549 3438 9.565213 CTTCGATTGAGATTAAGATTTTGCTTT 57.435 29.630 0.00 0.00 0.00 3.51
2558 3447 5.395324 GGACCACCTTCGATTGAGATTAAGA 60.395 44.000 0.00 0.00 0.00 2.10
2588 3477 5.045872 GCTTCAAGCACATTGTTCTTCTTT 58.954 37.500 3.89 0.00 41.89 2.52
2616 3505 4.931002 GGTCATGTGAATGATTTGGGTTTG 59.069 41.667 0.00 0.00 32.61 2.93
2686 3575 4.719273 TGGGCCATATATCATCCGTGAATA 59.281 41.667 0.00 0.00 38.01 1.75
2747 3636 3.759086 TCATGGCAAGTATTTTACGGCAA 59.241 39.130 0.00 0.00 36.18 4.52
2795 3687 5.762179 AGATGAGGTTGGTAGAACAATGA 57.238 39.130 0.00 0.00 32.24 2.57
2805 3697 4.706842 ACAACTTGTAGATGAGGTTGGT 57.293 40.909 0.00 0.00 40.75 3.67


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

AutoCloner maintained by Alex Coulton.