Multiple sequence alignment - TraesCS7B01G230800

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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 TraesCS7B01G230800 chr7B 100.000 6492 0 0 1 6492 433352686 433346195 0.000000e+00 11989
1 TraesCS7B01G230800 chr7D 96.420 6396 143 38 141 6492 417623292 417616939 0.000000e+00 10464
2 TraesCS7B01G230800 chr7D 89.241 158 10 3 1 158 417623843 417623693 2.390000e-44 191
3 TraesCS7B01G230800 chr7A 96.092 5502 176 14 579 6071 482490123 482484652 0.000000e+00 8933
4 TraesCS7B01G230800 chr7A 83.399 506 40 23 2 494 482569457 482568983 4.650000e-116 429
5 TraesCS7B01G230800 chr7A 86.139 101 13 1 138 238 673242661 673242562 2.480000e-19 108
6 TraesCS7B01G230800 chr6D 88.506 87 10 0 152 238 131933927 131934013 8.900000e-19 106
7 TraesCS7B01G230800 chr6D 88.506 87 10 0 152 238 303614561 303614647 8.900000e-19 106
8 TraesCS7B01G230800 chr6D 88.506 87 10 0 152 238 464274150 464274236 8.900000e-19 106
9 TraesCS7B01G230800 chr5D 88.506 87 10 0 152 238 482814526 482814440 8.900000e-19 106
10 TraesCS7B01G230800 chr4D 88.506 87 10 0 152 238 486777010 486777096 8.900000e-19 106
11 TraesCS7B01G230800 chr1D 88.506 87 10 0 152 238 272538845 272538931 8.900000e-19 106


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 TraesCS7B01G230800 chr7B 433346195 433352686 6491 True 11989.0 11989 100.0000 1 6492 1 chr7B.!!$R1 6491
1 TraesCS7B01G230800 chr7D 417616939 417623843 6904 True 5327.5 10464 92.8305 1 6492 2 chr7D.!!$R1 6491
2 TraesCS7B01G230800 chr7A 482484652 482490123 5471 True 8933.0 8933 96.0920 579 6071 1 chr7A.!!$R1 5492

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
32 33 0.806102 AACGAGACGATTGCATCCCG 60.806 55.000 0.00 0.00 0.00 5.14 F
72 73 0.897621 CCAAATCCAGGAGCCCAAAC 59.102 55.000 0.00 0.00 0.00 2.93 F
148 149 1.003835 GTTAGCTACCCCCTCCCCA 59.996 63.158 0.00 0.00 0.00 4.96 F
1049 1496 1.528309 CCCGACAACCAAAGCCTGT 60.528 57.895 0.00 0.00 0.00 4.00 F
2285 2737 0.393820 AACCCCAAGTGCATGCTTTG 59.606 50.000 20.33 20.92 0.00 2.77 F
3531 3990 0.462581 GACATGCAATCCCTCGAGCA 60.463 55.000 6.99 1.36 41.73 4.26 F
3667 4126 1.429463 CACGGCAGACCTTTAGACAC 58.571 55.000 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 2185 1.277842 TGGTTCGCAGGCTATGAAGAA 59.722 47.619 1.24 0.0 0.00 2.52 R
1889 2341 5.633830 ATGTGGAATTACAAGCAACTCAG 57.366 39.130 0.00 0.0 33.69 3.35 R
1973 2425 8.394971 TGAAAGAATCACAAGAAAATGCTCTA 57.605 30.769 0.00 0.0 31.50 2.43 R
2417 2870 2.919602 AGAGTTTAATCTTCCCCTGCCA 59.080 45.455 0.00 0.0 0.00 4.92 R
3651 4110 2.841442 AGTGTGTCTAAAGGTCTGCC 57.159 50.000 0.00 0.0 0.00 4.85 R
4416 4876 0.774096 TGGTCCAATGGAGGGGTTGA 60.774 55.000 0.27 0.0 29.39 3.18 R
5568 6028 0.036732 TCCCTTCACATCGCAGCTTT 59.963 50.000 0.00 0.0 0.00 3.51 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 5.900339 TTTATAACGAGACGATTGCATCC 57.100 39.130 0.00 0.00 0.00 3.51
31 32 2.218953 TAACGAGACGATTGCATCCC 57.781 50.000 0.00 0.00 0.00 3.85
32 33 0.806102 AACGAGACGATTGCATCCCG 60.806 55.000 0.00 0.00 0.00 5.14
33 34 1.226974 CGAGACGATTGCATCCCGT 60.227 57.895 8.02 8.02 39.41 5.28
35 36 3.719214 GACGATTGCATCCCGTCC 58.281 61.111 19.01 7.04 44.67 4.79
36 37 2.202878 ACGATTGCATCCCGTCCG 60.203 61.111 0.00 0.00 29.82 4.79
64 65 1.149101 GGGATAGGCCAAATCCAGGA 58.851 55.000 28.79 0.00 44.08 3.86
71 72 0.904394 GCCAAATCCAGGAGCCCAAA 60.904 55.000 0.00 0.00 0.00 3.28
72 73 0.897621 CCAAATCCAGGAGCCCAAAC 59.102 55.000 0.00 0.00 0.00 2.93
75 76 2.634453 CAAATCCAGGAGCCCAAACTTT 59.366 45.455 0.00 0.00 0.00 2.66
87 88 6.233905 AGCCCAAACTTTTGTTGTTAGAAT 57.766 33.333 1.21 0.00 42.67 2.40
110 111 9.160496 GAATGTCCATACAATGATCTATCTTCC 57.840 37.037 0.00 0.00 39.58 3.46
112 113 7.674120 TGTCCATACAATGATCTATCTTCCAG 58.326 38.462 0.00 0.00 30.91 3.86
148 149 1.003835 GTTAGCTACCCCCTCCCCA 59.996 63.158 0.00 0.00 0.00 4.96
213 630 4.591321 AAGAGCTTGTATCCCCATTGAA 57.409 40.909 0.00 0.00 0.00 2.69
214 631 4.591321 AGAGCTTGTATCCCCATTGAAA 57.409 40.909 0.00 0.00 0.00 2.69
239 656 5.970317 TGTTTGACATCTTGAATGCTCAT 57.030 34.783 0.00 0.00 0.00 2.90
247 664 6.989659 ACATCTTGAATGCTCATTGAAACTT 58.010 32.000 0.00 0.00 0.00 2.66
286 703 4.393062 TGCTCTTCTTATGCACTAGTTTGC 59.607 41.667 0.00 0.00 43.31 3.68
298 715 3.632145 CACTAGTTTGCACCTTTTCCACT 59.368 43.478 0.00 0.00 0.00 4.00
300 717 5.049405 CACTAGTTTGCACCTTTTCCACTAG 60.049 44.000 0.00 0.00 38.69 2.57
363 780 9.664332 CTGGAACTCCATAATAGATAAATCCTG 57.336 37.037 0.00 0.00 46.46 3.86
388 805 8.970020 TGATCTGGCATATGTAACAAAAATTCT 58.030 29.630 4.29 0.00 0.00 2.40
410 845 6.711277 TCTAAAATAGTCTCACAAGTGCCAT 58.289 36.000 0.00 0.00 0.00 4.40
412 847 5.886960 AAATAGTCTCACAAGTGCCATTC 57.113 39.130 0.00 0.00 0.00 2.67
418 853 5.069516 AGTCTCACAAGTGCCATTCATTTTT 59.930 36.000 0.00 0.00 0.00 1.94
452 887 1.669265 GCTAAGTATTGGCGGTTGGTC 59.331 52.381 0.00 0.00 44.35 4.02
454 889 2.279935 AAGTATTGGCGGTTGGTCAA 57.720 45.000 0.00 0.00 45.82 3.18
490 925 7.949903 TTTTAGACGCGCAAATATAATCCTA 57.050 32.000 5.73 0.00 0.00 2.94
507 942 5.997384 ATCCTATAAATGGTACTCGGACC 57.003 43.478 0.00 0.00 40.21 4.46
555 997 6.343716 AGAGGTGCTCTTATACATCATCTG 57.656 41.667 0.00 0.00 37.60 2.90
853 1300 2.307768 CATACCTAGGTTCTGCTCGGA 58.692 52.381 22.11 0.00 0.00 4.55
923 1370 1.589113 GGCTGTTGCGTCTCTCTCT 59.411 57.895 0.00 0.00 40.82 3.10
946 1393 2.047274 CCTGCTTCCCGCTTTCGA 60.047 61.111 0.00 0.00 40.11 3.71
959 1406 4.814771 CCCGCTTTCGATCTTAATAGGTTT 59.185 41.667 0.00 0.00 38.10 3.27
1008 1455 2.043604 ATCGATTCCAGATGGCCGCA 62.044 55.000 0.00 0.00 34.44 5.69
1048 1495 2.919494 GCCCGACAACCAAAGCCTG 61.919 63.158 0.00 0.00 0.00 4.85
1049 1496 1.528309 CCCGACAACCAAAGCCTGT 60.528 57.895 0.00 0.00 0.00 4.00
1332 1779 5.298527 TCTCCGTCCATGTATGTACTTAGTG 59.701 44.000 0.00 0.00 0.00 2.74
1337 1784 4.340097 TCCATGTATGTACTTAGTGGGACG 59.660 45.833 14.95 0.00 0.00 4.79
1542 1993 5.519927 GCAAGAGTTTGTGCAACTATGTTTT 59.480 36.000 0.00 0.00 46.53 2.43
1973 2425 1.558756 CTTCCTCTGGCCAGACAGAAT 59.441 52.381 32.00 0.00 46.05 2.40
2208 2660 2.970324 GACCACCGTGCTTTCGCA 60.970 61.111 0.00 0.00 45.60 5.10
2285 2737 0.393820 AACCCCAAGTGCATGCTTTG 59.606 50.000 20.33 20.92 0.00 2.77
2417 2870 9.796120 TGATAACTTCTTTCATTTTTGTTTCGT 57.204 25.926 0.00 0.00 0.00 3.85
2443 2896 5.570320 CAGGGGAAGATTAAACTCTTGGAA 58.430 41.667 0.00 0.00 35.63 3.53
2455 2908 4.632538 ACTCTTGGAACTTGAAAAACGG 57.367 40.909 0.00 0.00 0.00 4.44
2756 3211 2.158842 AGCATACAAGGCTCCTGATGAC 60.159 50.000 8.90 3.01 36.81 3.06
2853 3308 4.941263 TCAGTTTCAGTTTGCACTTGTACT 59.059 37.500 0.00 0.00 0.00 2.73
2859 3314 5.227908 TCAGTTTGCACTTGTACTAGTAGC 58.772 41.667 9.68 14.76 0.00 3.58
3137 3596 3.118956 AGAGAAATACCCAGAAGCGACTG 60.119 47.826 6.28 6.28 37.61 3.51
3493 3952 5.121611 TGGTGCTGTTTCGTATACATCTTTG 59.878 40.000 3.32 0.00 0.00 2.77
3526 3985 1.747355 CAGTTGGACATGCAATCCCTC 59.253 52.381 15.81 9.73 35.12 4.30
3531 3990 0.462581 GACATGCAATCCCTCGAGCA 60.463 55.000 6.99 1.36 41.73 4.26
3578 4037 6.429385 AGTTGAAACAAAACAAAAATGCTGGA 59.571 30.769 0.00 0.00 0.00 3.86
3667 4126 1.429463 CACGGCAGACCTTTAGACAC 58.571 55.000 0.00 0.00 0.00 3.67
4356 4816 2.071778 ATGCCAAGAAACACACCACT 57.928 45.000 0.00 0.00 0.00 4.00
4416 4876 1.212935 ACCTTCACAGCAGTTCCAAGT 59.787 47.619 0.00 0.00 0.00 3.16
4763 5223 1.000771 GGCCCCCAGTCTTTTCCTC 60.001 63.158 0.00 0.00 0.00 3.71
5005 5465 3.673746 TTCTCAAGTTCAGCAAACACG 57.326 42.857 5.00 0.00 40.56 4.49
5082 5542 3.775261 TTTTACCTTTAGGCCTCACGT 57.225 42.857 9.68 3.98 39.32 4.49
5402 5862 2.426024 CCACAGCAGAATCCATTTCCAG 59.574 50.000 0.00 0.00 34.67 3.86
5403 5863 2.097825 ACAGCAGAATCCATTTCCAGC 58.902 47.619 0.00 0.00 36.58 4.85
5520 5980 2.405559 ACTGAGGATCTCATGGCATCA 58.594 47.619 0.00 0.00 39.92 3.07
5536 5996 1.734465 CATCAGTTGGCTCGAAAGGAC 59.266 52.381 0.00 0.00 0.00 3.85
5568 6028 3.444029 TGTCATCTCTGTCCTGGAATCA 58.556 45.455 0.00 0.00 0.00 2.57
5663 6123 2.680841 TGTTTTGACAGAAGAACACCGG 59.319 45.455 0.00 0.00 0.00 5.28
5685 6145 3.330267 GTCGAAGGAGACATTTCTTGCT 58.670 45.455 0.00 0.00 40.65 3.91
5758 6218 1.677576 CCTGTGCTGTTTTGCTCTTCA 59.322 47.619 0.00 0.00 0.00 3.02
5813 6273 7.324856 TGCGTTTGTTTACAGCAATTTATGTAG 59.675 33.333 0.00 0.00 33.66 2.74
5836 6296 2.960170 CCTTGCTTCCAGTGCAGC 59.040 61.111 5.74 5.74 41.71 5.25
5962 6422 1.291132 CCCGAGTAGCTAAAAGCAGC 58.709 55.000 0.00 0.00 45.56 5.25
5963 6423 0.924090 CCGAGTAGCTAAAAGCAGCG 59.076 55.000 0.00 0.00 45.56 5.18
6023 6484 2.681344 GTGGTTCAAAAACGTGGAGTCT 59.319 45.455 0.00 0.00 36.16 3.24
6139 6607 3.674997 AGTTCATGTATGCCGTGTTTCT 58.325 40.909 0.00 0.00 0.00 2.52
6146 6614 6.700081 TCATGTATGCCGTGTTTCTATTACTC 59.300 38.462 0.00 0.00 0.00 2.59
6155 6623 6.455113 CCGTGTTTCTATTACTCGTTTCATGG 60.455 42.308 0.00 0.00 32.40 3.66
6171 6639 8.183536 TCGTTTCATGGTTATTTCAATCATCTG 58.816 33.333 0.00 0.00 0.00 2.90
6197 6665 1.455786 CTCGAACGTCACATGGTTCAC 59.544 52.381 11.51 0.00 41.97 3.18
6224 6692 1.602191 GTTAGCGGTTCAAACATGCG 58.398 50.000 0.00 0.00 37.05 4.73
6246 6714 4.054671 GGAGTCTCGTTCCAATCATCATC 58.945 47.826 0.00 0.00 34.74 2.92
6253 6721 6.266330 TCTCGTTCCAATCATCATCTATCAGT 59.734 38.462 0.00 0.00 0.00 3.41
6259 6727 8.455903 TCCAATCATCATCTATCAGTTTTTCC 57.544 34.615 0.00 0.00 0.00 3.13
6260 6728 8.054572 TCCAATCATCATCTATCAGTTTTTCCA 58.945 33.333 0.00 0.00 0.00 3.53
6261 6729 8.689061 CCAATCATCATCTATCAGTTTTTCCAA 58.311 33.333 0.00 0.00 0.00 3.53
6264 6732 8.055279 TCATCATCTATCAGTTTTTCCAAACC 57.945 34.615 0.00 0.00 43.08 3.27
6265 6733 7.890127 TCATCATCTATCAGTTTTTCCAAACCT 59.110 33.333 0.00 0.00 43.08 3.50
6266 6734 7.452880 TCATCTATCAGTTTTTCCAAACCTG 57.547 36.000 0.00 0.00 43.08 4.00
6267 6735 6.434028 TCATCTATCAGTTTTTCCAAACCTGG 59.566 38.462 0.00 0.00 43.08 4.45
6307 6775 4.254492 TGTTTGTAACAACTTTTTGGGGC 58.746 39.130 0.00 0.00 38.72 5.80
6326 6795 3.125316 GGGCAAGTTAGTGTTTCATCTCG 59.875 47.826 0.00 0.00 0.00 4.04
6332 6801 4.750098 AGTTAGTGTTTCATCTCGTGGTTG 59.250 41.667 0.00 0.00 0.00 3.77
6342 6811 1.067142 TCTCGTGGTTGGAAAGGATCG 60.067 52.381 0.00 0.00 0.00 3.69
6349 6818 3.835978 TGGTTGGAAAGGATCGAGAGTTA 59.164 43.478 0.00 0.00 0.00 2.24
6350 6819 4.285003 TGGTTGGAAAGGATCGAGAGTTAA 59.715 41.667 0.00 0.00 0.00 2.01
6361 6830 3.629087 TCGAGAGTTAAACTAGAGGGGG 58.371 50.000 0.00 0.00 0.00 5.40
6369 6838 0.252742 AACTAGAGGGGGTGGAGTGG 60.253 60.000 0.00 0.00 0.00 4.00
6388 6857 3.392616 GTGGGGGTGAATATGAGACTGAT 59.607 47.826 0.00 0.00 0.00 2.90
6389 6858 4.047166 TGGGGGTGAATATGAGACTGATT 58.953 43.478 0.00 0.00 0.00 2.57
6422 6891 8.881262 TGGTTTAATTTCTAAATTTTAGGGGCA 58.119 29.630 14.60 0.00 39.24 5.36
6435 6904 2.443958 AGGGGCAAAGAGGATAAAGC 57.556 50.000 0.00 0.00 0.00 3.51
6457 6930 4.352039 CACGTTCTCTATGCAATCTACGT 58.648 43.478 0.00 0.00 41.08 3.57
6458 6931 4.438145 CACGTTCTCTATGCAATCTACGTC 59.562 45.833 10.66 0.00 38.73 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.876342 GGACGGGATGCAATCGTCTC 60.876 60.000 26.72 18.25 46.86 3.36
31 32 2.067091 TATCCCTAGCGCAACGGACG 62.067 60.000 11.47 0.00 0.00 4.79
32 33 0.318784 CTATCCCTAGCGCAACGGAC 60.319 60.000 11.47 0.00 0.00 4.79
33 34 1.461091 CCTATCCCTAGCGCAACGGA 61.461 60.000 11.47 11.29 0.00 4.69
34 35 1.006102 CCTATCCCTAGCGCAACGG 60.006 63.158 11.47 6.40 0.00 4.44
35 36 1.664965 GCCTATCCCTAGCGCAACG 60.665 63.158 11.47 0.00 0.00 4.10
36 37 1.301795 GGCCTATCCCTAGCGCAAC 60.302 63.158 11.47 0.00 0.00 4.17
64 65 5.669164 TTCTAACAACAAAAGTTTGGGCT 57.331 34.783 8.55 0.00 42.34 5.19
71 72 8.458573 TGTATGGACATTCTAACAACAAAAGT 57.541 30.769 0.00 0.00 0.00 2.66
72 73 9.912634 ATTGTATGGACATTCTAACAACAAAAG 57.087 29.630 1.69 0.00 34.86 2.27
75 76 8.628630 TCATTGTATGGACATTCTAACAACAA 57.371 30.769 1.69 0.39 34.86 2.83
87 88 7.510343 TCTGGAAGATAGATCATTGTATGGACA 59.490 37.037 0.00 0.00 38.67 4.02
110 111 5.712152 AACTTTATTGCAGGAGGTTTCTG 57.288 39.130 0.00 0.00 35.49 3.02
112 113 5.416013 AGCTAACTTTATTGCAGGAGGTTTC 59.584 40.000 0.00 0.00 0.00 2.78
148 149 7.164803 GCTTCATCTCCAAAGGCTACTATAAT 58.835 38.462 0.00 0.00 0.00 1.28
213 630 6.152932 AGCATTCAAGATGTCAAACAAGTT 57.847 33.333 0.00 0.00 0.00 2.66
214 631 5.300034 TGAGCATTCAAGATGTCAAACAAGT 59.700 36.000 0.00 0.00 0.00 3.16
239 656 5.336150 TCAAGATGCCAAACAAGTTTCAA 57.664 34.783 0.00 0.00 0.00 2.69
247 664 3.159472 AGAGCATTCAAGATGCCAAACA 58.841 40.909 7.33 0.00 45.59 2.83
286 703 7.848128 TCCTAGTATTTCTAGTGGAAAAGGTG 58.152 38.462 13.91 2.93 45.56 4.00
287 704 8.625467 ATCCTAGTATTTCTAGTGGAAAAGGT 57.375 34.615 13.91 0.00 45.56 3.50
388 805 6.939730 TGAATGGCACTTGTGAGACTATTTTA 59.060 34.615 4.79 0.00 0.00 1.52
396 813 5.534207 AAAAATGAATGGCACTTGTGAGA 57.466 34.783 4.79 0.00 0.00 3.27
431 866 1.280998 ACCAACCGCCAATACTTAGCT 59.719 47.619 0.00 0.00 0.00 3.32
444 879 4.503741 AATGATTGTTCTTGACCAACCG 57.496 40.909 0.00 0.00 0.00 4.44
473 908 7.693952 ACCATTTATAGGATTATATTTGCGCG 58.306 34.615 0.00 0.00 0.00 6.86
487 922 5.078256 AGAGGTCCGAGTACCATTTATAGG 58.922 45.833 4.68 0.00 42.40 2.57
490 925 4.585162 CAGAGAGGTCCGAGTACCATTTAT 59.415 45.833 4.68 0.00 42.40 1.40
502 937 5.967088 TCTCTTAAAATTCAGAGAGGTCCG 58.033 41.667 3.51 0.00 40.56 4.79
503 938 7.560368 TGATCTCTTAAAATTCAGAGAGGTCC 58.440 38.462 16.37 8.42 46.86 4.46
505 940 9.972106 AATTGATCTCTTAAAATTCAGAGAGGT 57.028 29.630 11.48 7.44 46.86 3.85
568 1010 7.282450 GGGTTAGAGTACCTCCAAACAAATATG 59.718 40.741 0.00 0.00 38.30 1.78
569 1011 7.184022 AGGGTTAGAGTACCTCCAAACAAATAT 59.816 37.037 0.00 0.00 38.30 1.28
570 1012 6.502863 AGGGTTAGAGTACCTCCAAACAAATA 59.497 38.462 0.00 0.00 38.30 1.40
830 1277 1.681793 GAGCAGAACCTAGGTATGCGA 59.318 52.381 31.29 0.00 42.26 5.10
959 1406 4.723789 AGGAGAATTGAATCCTTGAGGCTA 59.276 41.667 0.00 0.00 43.62 3.93
1008 1455 5.221322 GGCAGGAGAAGATTGTTCAAGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
1332 1779 3.318275 TCTGAGAATGTGCTATACGTCCC 59.682 47.826 0.00 0.00 0.00 4.46
1337 1784 6.642707 AGGTACTCTGAGAATGTGCTATAC 57.357 41.667 12.44 0.02 0.00 1.47
1396 1847 2.878406 TCCTTTCCGCATTGCTAATAGC 59.122 45.455 5.12 5.12 42.82 2.97
1542 1993 5.181245 GCCTGAGTTTGCTAAAGATACACAA 59.819 40.000 0.00 0.00 0.00 3.33
1733 2185 1.277842 TGGTTCGCAGGCTATGAAGAA 59.722 47.619 1.24 0.00 0.00 2.52
1873 2325 8.480643 AGCAACTCAGTAAGATGTATTACAAC 57.519 34.615 0.00 0.00 37.98 3.32
1874 2326 8.935844 CAAGCAACTCAGTAAGATGTATTACAA 58.064 33.333 0.00 0.00 37.98 2.41
1875 2327 8.094548 ACAAGCAACTCAGTAAGATGTATTACA 58.905 33.333 0.00 0.00 37.98 2.41
1876 2328 8.480643 ACAAGCAACTCAGTAAGATGTATTAC 57.519 34.615 0.00 0.00 36.16 1.89
1878 2330 9.672673 ATTACAAGCAACTCAGTAAGATGTATT 57.327 29.630 0.00 0.00 30.72 1.89
1879 2331 9.672673 AATTACAAGCAACTCAGTAAGATGTAT 57.327 29.630 0.00 0.00 30.72 2.29
1880 2332 9.151471 GAATTACAAGCAACTCAGTAAGATGTA 57.849 33.333 0.00 0.00 30.72 2.29
1889 2341 5.633830 ATGTGGAATTACAAGCAACTCAG 57.366 39.130 0.00 0.00 33.69 3.35
1973 2425 8.394971 TGAAAGAATCACAAGAAAATGCTCTA 57.605 30.769 0.00 0.00 31.50 2.43
2208 2660 4.457466 ACGTTGTGAACAATAGAAAGGGT 58.543 39.130 0.00 0.00 38.24 4.34
2285 2737 8.547967 TTGATTGTACAACTCATTTCCTCTAC 57.452 34.615 11.22 0.00 0.00 2.59
2417 2870 2.919602 AGAGTTTAATCTTCCCCTGCCA 59.080 45.455 0.00 0.00 0.00 4.92
2443 2896 6.822442 ACCAATAATTTCCCGTTTTTCAAGT 58.178 32.000 0.00 0.00 0.00 3.16
2455 2908 9.841880 GAACAACTTCTCTTACCAATAATTTCC 57.158 33.333 0.00 0.00 0.00 3.13
2756 3211 6.640518 TGTCTCCTTAAGTAATGGCTTGTAG 58.359 40.000 0.97 0.00 0.00 2.74
2853 3308 7.223971 CACTACAAACAAGTGAAACAGCTACTA 59.776 37.037 0.00 0.00 45.89 1.82
2859 3314 5.106317 ACACCACTACAAACAAGTGAAACAG 60.106 40.000 4.84 0.00 45.89 3.16
3137 3596 6.529220 AGAATGACTCATTAATACCTCCTGC 58.471 40.000 4.16 0.00 33.90 4.85
3224 3683 7.334171 CCTGGCATATGATAAATGATGTAACGA 59.666 37.037 6.97 0.00 0.00 3.85
3493 3952 5.627499 TGTCCAACTGAATACTTTGCATC 57.373 39.130 0.00 0.00 0.00 3.91
3578 4037 7.346751 TCAAGAGCAAAAGATTAACAAAGGT 57.653 32.000 0.00 0.00 0.00 3.50
3651 4110 2.841442 AGTGTGTCTAAAGGTCTGCC 57.159 50.000 0.00 0.00 0.00 4.85
3756 4216 7.462571 TCGCTATCAGGATTACTTGCTAATA 57.537 36.000 0.00 0.00 0.00 0.98
3878 4338 5.639506 GCTGACACATGTATGTATATGTCCC 59.360 44.000 0.00 0.00 39.39 4.46
4356 4816 4.158786 TGATGGCTGAAATCCAGGAAAAA 58.841 39.130 0.00 0.00 43.13 1.94
4416 4876 0.774096 TGGTCCAATGGAGGGGTTGA 60.774 55.000 0.27 0.00 29.39 3.18
4693 5153 2.173569 AGGAGTGAAGTTTGCTCTTGGT 59.826 45.455 7.32 0.00 0.00 3.67
4763 5223 3.641434 AGGACCATGAGATGAAACTGG 57.359 47.619 0.00 0.00 0.00 4.00
5005 5465 5.186797 AGCTATAGATGTCTGATTGTAGCCC 59.813 44.000 3.21 0.00 35.19 5.19
5116 5576 4.751431 GCCTGAGCTCCCATTTGT 57.249 55.556 12.15 0.00 35.50 2.83
5233 5693 1.121407 TCCGAGCCTGACCCATATGG 61.121 60.000 15.41 15.41 41.37 2.74
5402 5862 1.300388 CACCTTGCCTGTTTGCAGC 60.300 57.895 0.00 0.00 43.21 5.25
5403 5863 1.364901 CCACCTTGCCTGTTTGCAG 59.635 57.895 0.00 0.00 43.21 4.41
5520 5980 2.046938 TCGTCCTTTCGAGCCAACT 58.953 52.632 0.00 0.00 34.85 3.16
5568 6028 0.036732 TCCCTTCACATCGCAGCTTT 59.963 50.000 0.00 0.00 0.00 3.51
5663 6123 2.416893 GCAAGAAATGTCTCCTTCGACC 59.583 50.000 0.00 0.00 30.70 4.79
5685 6145 5.425577 TGAACGTACAAATAGCTGCAAAA 57.574 34.783 1.02 0.00 0.00 2.44
5691 6151 5.585047 GGAGGATTTGAACGTACAAATAGCT 59.415 40.000 0.00 0.00 46.18 3.32
5758 6218 2.084546 GGGTATGAGTTTCGCTTGCTT 58.915 47.619 0.00 0.00 0.00 3.91
5813 6273 1.160137 CACTGGAAGCAAGGCAGTAC 58.840 55.000 0.00 0.00 37.60 2.73
5836 6296 4.402155 TGCTGGCACAAGAATATTTTAGGG 59.598 41.667 0.00 0.00 38.70 3.53
5962 6422 2.104967 TGGGTTAGTGGATAGGACACG 58.895 52.381 0.00 0.00 43.41 4.49
5963 6423 3.518303 ACTTGGGTTAGTGGATAGGACAC 59.482 47.826 0.00 0.00 39.10 3.67
6023 6484 5.240403 TCATGACAAACGATGATCAAAACCA 59.760 36.000 0.00 0.00 0.00 3.67
6078 6546 5.172205 TCCAAGCAAACAAACTTACCAAAC 58.828 37.500 0.00 0.00 0.00 2.93
6146 6614 8.183536 TCAGATGATTGAAATAACCATGAAACG 58.816 33.333 0.00 0.00 0.00 3.60
6155 6623 8.124823 TCGAGCAAATCAGATGATTGAAATAAC 58.875 33.333 8.76 0.00 43.41 1.89
6162 6630 4.201753 ACGTTCGAGCAAATCAGATGATTG 60.202 41.667 8.76 5.11 43.41 2.67
6171 6639 2.474526 CCATGTGACGTTCGAGCAAATC 60.475 50.000 0.00 0.00 0.00 2.17
6197 6665 2.510691 AACCGCTAACGCCATCCG 60.511 61.111 0.00 0.00 44.21 4.18
6224 6692 3.526931 TGATGATTGGAACGAGACTCC 57.473 47.619 0.00 0.00 0.00 3.85
6259 6727 2.153366 AAAGCGCAAATCCAGGTTTG 57.847 45.000 11.47 0.00 41.02 2.93
6260 6728 4.021544 TGATTAAAGCGCAAATCCAGGTTT 60.022 37.500 20.50 8.62 38.77 3.27
6261 6729 3.509575 TGATTAAAGCGCAAATCCAGGTT 59.490 39.130 20.50 0.00 32.25 3.50
6262 6730 3.088532 TGATTAAAGCGCAAATCCAGGT 58.911 40.909 20.50 0.00 32.25 4.00
6263 6731 3.781079 TGATTAAAGCGCAAATCCAGG 57.219 42.857 20.50 0.00 32.25 4.45
6264 6732 5.104374 ACAATGATTAAAGCGCAAATCCAG 58.896 37.500 20.50 14.68 32.25 3.86
6265 6733 5.070770 ACAATGATTAAAGCGCAAATCCA 57.929 34.783 20.50 12.67 32.25 3.41
6266 6734 6.128580 ACAAACAATGATTAAAGCGCAAATCC 60.129 34.615 20.50 8.92 32.25 3.01
6267 6735 6.820459 ACAAACAATGATTAAAGCGCAAATC 58.180 32.000 11.47 15.82 33.57 2.17
6268 6736 6.783892 ACAAACAATGATTAAAGCGCAAAT 57.216 29.167 11.47 6.23 0.00 2.32
6269 6737 7.222805 TGTTACAAACAATGATTAAAGCGCAAA 59.777 29.630 11.47 0.31 38.72 3.68
6270 6738 6.697455 TGTTACAAACAATGATTAAAGCGCAA 59.303 30.769 11.47 0.00 38.72 4.85
6271 6739 6.209361 TGTTACAAACAATGATTAAAGCGCA 58.791 32.000 11.47 0.00 38.72 6.09
6272 6740 6.683090 TGTTACAAACAATGATTAAAGCGC 57.317 33.333 0.00 0.00 38.72 5.92
6303 6771 3.421844 AGATGAAACACTAACTTGCCCC 58.578 45.455 0.00 0.00 0.00 5.80
6304 6772 3.125316 CGAGATGAAACACTAACTTGCCC 59.875 47.826 0.00 0.00 0.00 5.36
6307 6775 4.750098 ACCACGAGATGAAACACTAACTTG 59.250 41.667 0.00 0.00 0.00 3.16
6326 6795 2.028020 ACTCTCGATCCTTTCCAACCAC 60.028 50.000 0.00 0.00 0.00 4.16
6332 6801 7.098074 TCTAGTTTAACTCTCGATCCTTTCC 57.902 40.000 0.00 0.00 0.00 3.13
6342 6811 3.451540 CCACCCCCTCTAGTTTAACTCTC 59.548 52.174 0.00 0.00 0.00 3.20
6349 6818 1.657804 CACTCCACCCCCTCTAGTTT 58.342 55.000 0.00 0.00 0.00 2.66
6350 6819 0.252742 CCACTCCACCCCCTCTAGTT 60.253 60.000 0.00 0.00 0.00 2.24
6361 6830 1.843851 TCATATTCACCCCCACTCCAC 59.156 52.381 0.00 0.00 0.00 4.02
6397 6866 9.727859 TTGCCCCTAAAATTTAGAAATTAAACC 57.272 29.630 13.87 0.00 37.62 3.27
6412 6881 4.709886 GCTTTATCCTCTTTGCCCCTAAAA 59.290 41.667 0.00 0.00 0.00 1.52
6413 6882 4.264172 TGCTTTATCCTCTTTGCCCCTAAA 60.264 41.667 0.00 0.00 0.00 1.85
6414 6883 3.268334 TGCTTTATCCTCTTTGCCCCTAA 59.732 43.478 0.00 0.00 0.00 2.69
6415 6884 2.849943 TGCTTTATCCTCTTTGCCCCTA 59.150 45.455 0.00 0.00 0.00 3.53
6416 6885 1.640670 TGCTTTATCCTCTTTGCCCCT 59.359 47.619 0.00 0.00 0.00 4.79
6417 6886 1.751351 GTGCTTTATCCTCTTTGCCCC 59.249 52.381 0.00 0.00 0.00 5.80
6418 6887 1.401905 CGTGCTTTATCCTCTTTGCCC 59.598 52.381 0.00 0.00 0.00 5.36
6422 6891 5.153950 AGAGAACGTGCTTTATCCTCTTT 57.846 39.130 0.00 0.00 0.00 2.52
6435 6904 4.352039 ACGTAGATTGCATAGAGAACGTG 58.648 43.478 10.37 0.00 40.43 4.49
6457 6930 7.284919 TGCTTATCATATAGGTTGTTCTCGA 57.715 36.000 0.00 0.00 0.00 4.04
6458 6931 7.946655 TTGCTTATCATATAGGTTGTTCTCG 57.053 36.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.