Multiple sequence alignment - TraesCS1B01G127800

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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 TraesCS1B01G127800 chr1B 100.000 3149 0 0 1 3149 156606754 156603606 0.000000e+00 5816.0
1 TraesCS1B01G127800 chr1B 91.209 91 6 2 1 89 301659008 301659098 4.270000e-24 122.0
2 TraesCS1B01G127800 chr1D 92.138 2442 168 16 232 2654 96904935 96907371 0.000000e+00 3424.0
3 TraesCS1B01G127800 chr1A 91.826 2092 159 9 71 2154 91415487 91417574 0.000000e+00 2905.0
4 TraesCS1B01G127800 chr1A 92.864 1023 61 5 2138 3149 91417894 91418915 0.000000e+00 1474.0
5 TraesCS1B01G127800 chr1A 96.154 78 2 1 1 77 446561023 446560946 3.300000e-25 126.0
6 TraesCS1B01G127800 chr3B 96.296 81 2 1 1 80 252783562 252783642 7.090000e-27 132.0
7 TraesCS1B01G127800 chr7A 97.403 77 1 1 1 76 194450939 194451015 2.550000e-26 130.0
8 TraesCS1B01G127800 chr2D 95.062 81 4 0 1 81 143502638 143502558 9.170000e-26 128.0
9 TraesCS1B01G127800 chr7B 96.154 78 2 1 1 77 562187598 562187521 3.300000e-25 126.0
10 TraesCS1B01G127800 chr7B 91.011 89 6 2 1 88 228236304 228236391 5.520000e-23 119.0
11 TraesCS1B01G127800 chr2B 96.154 78 2 1 1 77 529643539 529643462 3.300000e-25 126.0
12 TraesCS1B01G127800 chr5D 89.583 96 7 3 1 94 306161339 306161245 5.520000e-23 119.0
13 TraesCS1B01G127800 chr5D 93.182 44 3 0 3039 3082 458874290 458874247 7.290000e-07 65.8
14 TraesCS1B01G127800 chr5D 93.023 43 3 0 3040 3082 499856368 499856410 2.620000e-06 63.9
15 TraesCS1B01G127800 chr5B 95.349 43 2 0 3040 3082 531189215 531189257 5.640000e-08 69.4
16 TraesCS1B01G127800 chr5B 93.023 43 3 0 3040 3082 514682784 514682826 2.620000e-06 63.9
17 TraesCS1B01G127800 chr5A 95.238 42 2 0 3041 3082 447372063 447372104 2.030000e-07 67.6
18 TraesCS1B01G127800 chr5A 93.023 43 3 0 3039 3081 487696661 487696703 2.620000e-06 63.9
19 TraesCS1B01G127800 chrUn 95.000 40 2 0 3043 3082 69983141 69983180 2.620000e-06 63.9
20 TraesCS1B01G127800 chr2A 95.000 40 2 0 3043 3082 623542361 623542322 2.620000e-06 63.9


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 TraesCS1B01G127800 chr1B 156603606 156606754 3148 True 5816.0 5816 100.000 1 3149 1 chr1B.!!$R1 3148
1 TraesCS1B01G127800 chr1D 96904935 96907371 2436 False 3424.0 3424 92.138 232 2654 1 chr1D.!!$F1 2422
2 TraesCS1B01G127800 chr1A 91415487 91418915 3428 False 2189.5 2905 92.345 71 3149 2 chr1A.!!$F1 3078

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
492 496 0.108281 GTCGAAAGCCAGTCTACCCC 60.108 60.0 0.0 0.0 0.0 4.95 F
1572 1580 0.107410 TTGTCCAAGGTTGTGTCGCT 60.107 50.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1790 0.161658 CGCGCACTAGCATATTTCCG 59.838 55.0 8.75 0.0 42.27 4.30 R
2696 3053 0.246360 GCCCAGGCCACAATACAAAC 59.754 55.0 5.01 0.0 34.56 2.93 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
23 24 6.957920 TGCTATGCATCTCCTAGATAGATC 57.042 41.667 0.19 0.00 32.12 2.75
24 25 6.671605 TGCTATGCATCTCCTAGATAGATCT 58.328 40.000 0.19 0.00 32.12 2.75
25 26 7.124721 TGCTATGCATCTCCTAGATAGATCTT 58.875 38.462 0.19 0.00 32.12 2.40
26 27 7.068470 TGCTATGCATCTCCTAGATAGATCTTG 59.932 40.741 0.19 0.00 32.12 3.02
27 28 5.657826 TGCATCTCCTAGATAGATCTTGC 57.342 43.478 0.00 0.69 38.32 4.01
28 29 5.082425 TGCATCTCCTAGATAGATCTTGCA 58.918 41.667 0.00 3.73 39.47 4.08
29 30 5.720520 TGCATCTCCTAGATAGATCTTGCAT 59.279 40.000 0.00 0.00 37.90 3.96
30 31 6.044046 GCATCTCCTAGATAGATCTTGCATG 58.956 44.000 0.00 0.00 38.32 4.06
31 32 6.127394 GCATCTCCTAGATAGATCTTGCATGA 60.127 42.308 0.00 4.57 38.32 3.07
32 33 7.485810 CATCTCCTAGATAGATCTTGCATGAG 58.514 42.308 0.00 1.23 38.32 2.90
33 34 5.418524 TCTCCTAGATAGATCTTGCATGAGC 59.581 44.000 9.67 9.67 38.32 4.26
34 35 4.157472 TCCTAGATAGATCTTGCATGAGCG 59.843 45.833 11.64 0.00 40.02 5.03
35 36 4.082300 CCTAGATAGATCTTGCATGAGCGT 60.082 45.833 11.64 5.52 40.02 5.07
36 37 5.124617 CCTAGATAGATCTTGCATGAGCGTA 59.875 44.000 11.64 6.01 40.02 4.42
37 38 5.058149 AGATAGATCTTGCATGAGCGTAG 57.942 43.478 11.64 0.00 46.23 3.51
38 39 4.522405 AGATAGATCTTGCATGAGCGTAGT 59.478 41.667 11.64 0.00 46.23 2.73
39 40 5.707764 AGATAGATCTTGCATGAGCGTAGTA 59.292 40.000 11.64 0.46 46.23 1.82
40 41 4.655762 AGATCTTGCATGAGCGTAGTAA 57.344 40.909 11.64 0.00 46.23 2.24
41 42 5.207110 AGATCTTGCATGAGCGTAGTAAT 57.793 39.130 11.64 0.00 46.23 1.89
42 43 5.605534 AGATCTTGCATGAGCGTAGTAATT 58.394 37.500 11.64 0.00 46.23 1.40
43 44 6.051717 AGATCTTGCATGAGCGTAGTAATTT 58.948 36.000 11.64 0.00 46.23 1.82
44 45 6.540189 AGATCTTGCATGAGCGTAGTAATTTT 59.460 34.615 11.64 0.00 46.23 1.82
45 46 6.494893 TCTTGCATGAGCGTAGTAATTTTT 57.505 33.333 0.00 0.00 46.23 1.94
67 68 6.724694 TTTGAAATTGCATGCTACATTTCC 57.275 33.333 28.57 19.14 0.00 3.13
68 69 4.757594 TGAAATTGCATGCTACATTTCCC 58.242 39.130 28.57 17.09 0.00 3.97
69 70 4.222366 TGAAATTGCATGCTACATTTCCCA 59.778 37.500 28.57 18.57 0.00 4.37
72 73 2.523245 TGCATGCTACATTTCCCAACA 58.477 42.857 20.33 0.00 0.00 3.33
81 82 7.327214 TGCTACATTTCCCAACAATATTTTCC 58.673 34.615 0.00 0.00 0.00 3.13
153 154 9.681692 TTTTGAAAATGCGATCATAATATGGAG 57.318 29.630 0.00 0.00 31.46 3.86
160 161 6.809869 TGCGATCATAATATGGAGTAGATGG 58.190 40.000 0.00 0.00 0.00 3.51
162 163 6.920758 GCGATCATAATATGGAGTAGATGGAC 59.079 42.308 0.00 0.00 0.00 4.02
173 174 3.970640 GAGTAGATGGACCAGGAAGGATT 59.029 47.826 0.00 0.00 41.22 3.01
210 213 2.461695 TCCTCCTTGTGAGAGATGACC 58.538 52.381 0.00 0.00 44.42 4.02
212 215 1.484240 CTCCTTGTGAGAGATGACCCC 59.516 57.143 0.00 0.00 44.42 4.95
214 217 1.065854 CCTTGTGAGAGATGACCCCAC 60.066 57.143 0.00 0.00 0.00 4.61
215 218 1.625315 CTTGTGAGAGATGACCCCACA 59.375 52.381 0.00 0.00 36.15 4.17
216 219 1.956869 TGTGAGAGATGACCCCACAT 58.043 50.000 0.00 0.00 33.42 3.21
217 220 1.556451 TGTGAGAGATGACCCCACATG 59.444 52.381 0.00 0.00 33.42 3.21
224 227 1.874299 ATGACCCCACATGTTCCCCC 61.874 60.000 0.00 0.00 0.00 5.40
257 260 5.710567 ACCACTTATGTTAAGCTTTTCTCCC 59.289 40.000 3.20 0.00 0.00 4.30
270 273 3.522731 CTCCCGTCGCTCTCCCTG 61.523 72.222 0.00 0.00 0.00 4.45
350 353 7.339721 CCCCTTCTTTCTTCCTAGGAATAAAAC 59.660 40.741 26.34 0.00 32.50 2.43
418 422 1.447838 CTTAGCGGCGCTTGGAGAA 60.448 57.895 40.77 25.47 40.44 2.87
419 423 1.424493 CTTAGCGGCGCTTGGAGAAG 61.424 60.000 40.77 30.14 40.44 2.85
455 459 2.642139 TTCGTCGTCCACCTTCATAC 57.358 50.000 0.00 0.00 0.00 2.39
483 487 3.811083 TGACCTTTAAAGTCGAAAGCCA 58.189 40.909 14.03 0.00 37.04 4.75
490 494 2.745515 AAGTCGAAAGCCAGTCTACC 57.254 50.000 0.00 0.00 0.00 3.18
492 496 0.108281 GTCGAAAGCCAGTCTACCCC 60.108 60.000 0.00 0.00 0.00 4.95
507 511 5.964477 AGTCTACCCCACATTGAATCTTCTA 59.036 40.000 0.00 0.00 0.00 2.10
598 602 4.260784 GGCTACATGCTTTTATGTCCTTCG 60.261 45.833 0.00 0.00 41.31 3.79
621 625 5.046304 CGGTGTATCCCAATCTTCATATCCT 60.046 44.000 0.00 0.00 0.00 3.24
637 641 2.747686 CTACCCCACACCAACGCT 59.252 61.111 0.00 0.00 0.00 5.07
641 645 2.746277 CCCACACCAACGCTAGCC 60.746 66.667 9.66 0.00 0.00 3.93
678 683 2.432456 TGCGACGTGTCCATCTGC 60.432 61.111 0.00 0.00 0.00 4.26
756 761 5.838521 AGGGTCCTATTTGCAAAAAGAAGAA 59.161 36.000 17.19 0.00 0.00 2.52
757 762 6.326323 AGGGTCCTATTTGCAAAAAGAAGAAA 59.674 34.615 17.19 1.60 0.00 2.52
849 856 6.403049 GGACCCTTGTTACATTAAAAATGGG 58.597 40.000 4.78 0.00 33.31 4.00
870 877 1.241315 AAAACAAGGATCCGGGCGTG 61.241 55.000 5.98 3.66 0.00 5.34
912 919 6.741724 AGGAAGGAAGGGAAATTAATTAGCA 58.258 36.000 0.01 0.00 0.00 3.49
923 930 5.874897 AATTAATTAGCACATGCCCACAT 57.125 34.783 0.00 0.00 43.38 3.21
926 933 6.975196 TTAATTAGCACATGCCCACATTAT 57.025 33.333 0.00 0.00 43.38 1.28
932 939 3.319972 GCACATGCCCACATTATTCATCT 59.680 43.478 0.00 0.00 32.87 2.90
987 995 4.240881 TCTAAGATTGCAAGCCTCCAAT 57.759 40.909 11.83 0.00 34.57 3.16
1098 1106 3.099141 CCTTGATTGTTACATGGCCCTT 58.901 45.455 0.00 0.00 0.00 3.95
1101 1109 2.290641 TGATTGTTACATGGCCCTTCGT 60.291 45.455 0.00 0.00 0.00 3.85
1157 1165 5.281314 AGACCCCAAGAATACTCTACACAT 58.719 41.667 0.00 0.00 0.00 3.21
1167 1175 0.456221 CTCTACACATCCGCTTCCGT 59.544 55.000 0.00 0.00 0.00 4.69
1180 1188 2.372040 CTTCCGTCCACACCGTTGGA 62.372 60.000 0.00 0.00 43.83 3.53
1239 1247 2.094649 CCTTCTAGTGAACACCGTCTCC 60.095 54.545 1.11 0.00 0.00 3.71
1464 1472 0.543749 GCCTTGTCCTCTACTGCCAT 59.456 55.000 0.00 0.00 0.00 4.40
1499 1507 2.196997 TACATGGCCAGCCCTGACAC 62.197 60.000 19.20 0.00 35.66 3.67
1503 1511 4.648626 GCCAGCCCTGACACTGCA 62.649 66.667 0.00 0.00 32.37 4.41
1572 1580 0.107410 TTGTCCAAGGTTGTGTCGCT 60.107 50.000 0.00 0.00 0.00 4.93
1575 1583 0.107410 TCCAAGGTTGTGTCGCTGTT 60.107 50.000 0.00 0.00 0.00 3.16
1594 1602 3.168528 ACGGCCACCAAGGACTGT 61.169 61.111 2.24 0.00 46.64 3.55
1613 1621 3.050275 GCCACCACTTCCTGCGAC 61.050 66.667 0.00 0.00 0.00 5.19
1632 1640 1.741770 GGTTGTCGCCAAGATCGCT 60.742 57.895 0.00 0.00 0.00 4.93
1654 1662 3.891366 TGATCTATTGACTCCGCTCATCA 59.109 43.478 0.00 0.00 0.00 3.07
1688 1696 4.566278 CCCTGACATTCAGTTGGATTCTCA 60.566 45.833 2.63 0.00 42.80 3.27
1745 1753 1.895798 TCTGGTCATCTTCAAGCTCGT 59.104 47.619 0.00 0.00 0.00 4.18
1782 1790 0.468585 TCAAGATGGATGGCATGGGC 60.469 55.000 3.81 0.00 40.13 5.36
1788 1796 1.833934 GGATGGCATGGGCGGAAAT 60.834 57.895 3.81 0.00 42.47 2.17
1794 1802 1.533625 GCATGGGCGGAAATATGCTA 58.466 50.000 0.00 0.00 41.89 3.49
1884 1892 1.474498 GCCGATAAGTTCCCGTCCATT 60.474 52.381 0.00 0.00 0.00 3.16
1908 1916 3.019564 AGCCAATTGCATCTACTTCACC 58.980 45.455 0.00 0.00 44.83 4.02
1914 1922 1.281899 GCATCTACTTCACCGAGTGC 58.718 55.000 0.00 0.00 32.98 4.40
1929 1937 2.353704 CGAGTGCCTAAGTTCACCATCA 60.354 50.000 0.00 0.00 33.90 3.07
1932 1940 3.146066 GTGCCTAAGTTCACCATCAACA 58.854 45.455 0.00 0.00 0.00 3.33
1938 1946 6.406370 CCTAAGTTCACCATCAACAGACATA 58.594 40.000 0.00 0.00 0.00 2.29
1939 1947 7.050377 CCTAAGTTCACCATCAACAGACATAT 58.950 38.462 0.00 0.00 0.00 1.78
1973 1983 2.798847 ACGGAGAACAAGTTAAGAACGC 59.201 45.455 0.00 0.00 36.23 4.84
1980 1990 3.740115 ACAAGTTAAGAACGCCATGAGT 58.260 40.909 0.00 0.00 36.23 3.41
1982 1992 3.402628 AGTTAAGAACGCCATGAGTGT 57.597 42.857 0.00 0.00 42.41 3.55
2034 2044 1.374505 CATGCCCGCCTTTTTGTGG 60.375 57.895 0.00 0.00 35.60 4.17
2049 2059 2.602257 TGTGGCATTCTATGACCGAG 57.398 50.000 0.00 0.00 37.55 4.63
2070 2080 2.449464 CATCCCTGCACCATCTTTCAA 58.551 47.619 0.00 0.00 0.00 2.69
2118 2128 2.079158 CAATCTGGTCAAGCGTCACAT 58.921 47.619 0.00 0.00 0.00 3.21
2162 2508 4.408182 TTCTTTAGAGGCTCCATACTGC 57.592 45.455 11.71 0.00 0.00 4.40
2171 2517 3.084786 GGCTCCATACTGCCCAAATATC 58.915 50.000 0.00 0.00 43.11 1.63
2269 2615 9.286170 TGTGTTGTGTTAAGCTTTATATGGTTA 57.714 29.630 3.20 0.00 0.00 2.85
2270 2616 9.769093 GTGTTGTGTTAAGCTTTATATGGTTAG 57.231 33.333 3.20 0.00 0.00 2.34
2347 2701 2.237392 ACTGGCTGGGTCTTGATAGTTC 59.763 50.000 0.00 0.00 0.00 3.01
2432 2786 5.391629 GCTTTGGTGGTGCTAGTTTATGTAC 60.392 44.000 0.00 0.00 0.00 2.90
2452 2806 5.937540 TGTACCATGTCCATGTCTGTTTTAG 59.062 40.000 6.53 0.00 37.11 1.85
2637 2994 7.509659 TGTCTACCTTTCTTTCTTTCCTCTACT 59.490 37.037 0.00 0.00 0.00 2.57
2638 2995 8.369424 GTCTACCTTTCTTTCTTTCCTCTACTT 58.631 37.037 0.00 0.00 0.00 2.24
2715 3072 0.246360 GTTTGTATTGTGGCCTGGGC 59.754 55.000 14.23 14.23 41.06 5.36
2736 3093 4.439057 GCGGATAGTTGTGTCAAATCCTA 58.561 43.478 9.84 0.00 35.06 2.94
2814 3171 8.615705 TCTACTGTCCAGGATATATGAGTGTAT 58.384 37.037 0.00 0.00 0.00 2.29
2818 3175 9.862371 CTGTCCAGGATATATGAGTGTATTTAC 57.138 37.037 0.00 0.00 0.00 2.01
2820 3177 8.737175 GTCCAGGATATATGAGTGTATTTACGA 58.263 37.037 0.00 0.00 0.00 3.43
2829 3186 5.388111 TGAGTGTATTTACGAAGAGTCACG 58.612 41.667 7.92 7.92 0.00 4.35
2840 3197 6.211664 ACGAAGAGTCACGAATACAAAAAG 57.788 37.500 14.72 0.00 0.00 2.27
2857 3214 4.746535 AAAAGGTTTGTCGGACCAAATT 57.253 36.364 5.55 0.00 39.71 1.82
2941 3300 3.232213 TGCCTAGTGCTTTCTTACTCG 57.768 47.619 5.06 0.00 42.00 4.18
2978 3337 4.883083 TCACAAACATGGTAGACACTCTC 58.117 43.478 0.00 0.00 0.00 3.20
2980 3339 5.773176 TCACAAACATGGTAGACACTCTCTA 59.227 40.000 0.00 0.00 0.00 2.43
2998 3358 4.894114 TCTCTAGTGTTAGTAAGATGGGGC 59.106 45.833 0.00 0.00 0.00 5.80
3023 3383 4.141233 AGATTGCACAAAAGCCAAAAGT 57.859 36.364 0.00 0.00 0.00 2.66
3026 3386 3.540314 TGCACAAAAGCCAAAAGTCAT 57.460 38.095 0.00 0.00 0.00 3.06
3093 3453 5.584253 TTTAGATCACTGTGGAGTAGCTC 57.416 43.478 8.11 0.00 0.00 4.09
3095 3455 2.757868 AGATCACTGTGGAGTAGCTCAC 59.242 50.000 8.11 0.00 31.08 3.51
3097 3457 2.529632 TCACTGTGGAGTAGCTCACAT 58.470 47.619 8.11 0.00 31.08 3.21
3145 3505 7.216973 ACTCCCGCTATAAATAGTAGTTGAG 57.783 40.000 0.00 0.00 32.96 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.671605 AGATCTATCTAGGAGATGCATAGCA 58.328 40.000 0.00 0.00 38.03 3.49
2 3 7.068470 TGCAAGATCTATCTAGGAGATGCATAG 59.932 40.741 0.00 0.00 37.90 2.23
3 4 6.894103 TGCAAGATCTATCTAGGAGATGCATA 59.106 38.462 0.00 0.00 37.90 3.14
4 5 5.720520 TGCAAGATCTATCTAGGAGATGCAT 59.279 40.000 0.00 0.00 37.90 3.96
5 6 5.082425 TGCAAGATCTATCTAGGAGATGCA 58.918 41.667 11.48 12.75 39.47 3.96
6 7 5.657826 TGCAAGATCTATCTAGGAGATGC 57.342 43.478 11.48 10.87 35.37 3.91
7 8 7.407393 TCATGCAAGATCTATCTAGGAGATG 57.593 40.000 11.48 2.82 35.37 2.90
8 9 6.097270 GCTCATGCAAGATCTATCTAGGAGAT 59.903 42.308 12.23 7.55 37.67 2.75
9 10 5.418524 GCTCATGCAAGATCTATCTAGGAGA 59.581 44.000 12.23 0.00 35.76 3.71
10 11 5.653507 GCTCATGCAAGATCTATCTAGGAG 58.346 45.833 0.00 1.35 35.76 3.69
11 12 4.157472 CGCTCATGCAAGATCTATCTAGGA 59.843 45.833 0.00 0.00 39.64 2.94
13 14 5.058149 ACGCTCATGCAAGATCTATCTAG 57.942 43.478 0.00 0.00 39.64 2.43
15 16 4.522405 ACTACGCTCATGCAAGATCTATCT 59.478 41.667 0.00 0.00 39.64 1.98
16 17 4.804108 ACTACGCTCATGCAAGATCTATC 58.196 43.478 0.00 0.00 39.64 2.08
17 18 4.862902 ACTACGCTCATGCAAGATCTAT 57.137 40.909 0.00 0.00 39.64 1.98
18 19 5.767816 TTACTACGCTCATGCAAGATCTA 57.232 39.130 0.00 0.00 39.64 1.98
19 20 4.655762 TTACTACGCTCATGCAAGATCT 57.344 40.909 0.00 0.00 39.64 2.75
20 21 5.914085 AATTACTACGCTCATGCAAGATC 57.086 39.130 0.00 0.00 39.64 2.75
21 22 6.683974 AAAATTACTACGCTCATGCAAGAT 57.316 33.333 0.00 0.00 39.64 2.40
22 23 6.494893 AAAAATTACTACGCTCATGCAAGA 57.505 33.333 0.00 0.00 39.64 3.02
42 43 7.308469 GGGAAATGTAGCATGCAATTTCAAAAA 60.308 33.333 32.13 9.38 33.52 1.94
43 44 6.149142 GGGAAATGTAGCATGCAATTTCAAAA 59.851 34.615 32.13 10.48 33.52 2.44
44 45 5.642919 GGGAAATGTAGCATGCAATTTCAAA 59.357 36.000 32.13 11.69 33.52 2.69
45 46 5.177326 GGGAAATGTAGCATGCAATTTCAA 58.823 37.500 32.13 12.87 33.52 2.69
46 47 4.222366 TGGGAAATGTAGCATGCAATTTCA 59.778 37.500 32.13 21.46 33.52 2.69
47 48 4.757594 TGGGAAATGTAGCATGCAATTTC 58.242 39.130 28.05 28.05 31.62 2.17
48 49 4.822685 TGGGAAATGTAGCATGCAATTT 57.177 36.364 21.98 20.58 31.62 1.82
49 50 4.020396 TGTTGGGAAATGTAGCATGCAATT 60.020 37.500 21.98 13.44 31.62 2.32
50 51 3.514706 TGTTGGGAAATGTAGCATGCAAT 59.485 39.130 21.98 7.61 31.62 3.56
51 52 2.896044 TGTTGGGAAATGTAGCATGCAA 59.104 40.909 21.98 5.23 31.62 4.08
52 53 2.523245 TGTTGGGAAATGTAGCATGCA 58.477 42.857 21.98 2.77 33.12 3.96
53 54 3.591196 TTGTTGGGAAATGTAGCATGC 57.409 42.857 10.51 10.51 0.00 4.06
54 55 8.721019 AAAATATTGTTGGGAAATGTAGCATG 57.279 30.769 0.00 0.00 0.00 4.06
55 56 7.986889 GGAAAATATTGTTGGGAAATGTAGCAT 59.013 33.333 0.00 0.00 0.00 3.79
56 57 7.180051 AGGAAAATATTGTTGGGAAATGTAGCA 59.820 33.333 0.00 0.00 0.00 3.49
57 58 7.555965 AGGAAAATATTGTTGGGAAATGTAGC 58.444 34.615 0.00 0.00 0.00 3.58
58 59 9.369904 CAAGGAAAATATTGTTGGGAAATGTAG 57.630 33.333 0.00 0.00 0.00 2.74
59 60 8.875168 ACAAGGAAAATATTGTTGGGAAATGTA 58.125 29.630 0.00 0.00 36.23 2.29
60 61 7.744733 ACAAGGAAAATATTGTTGGGAAATGT 58.255 30.769 0.00 0.00 36.23 2.71
61 62 8.620116 AACAAGGAAAATATTGTTGGGAAATG 57.380 30.769 2.74 0.00 45.38 2.32
72 73 6.418057 TTGCTCCACAACAAGGAAAATATT 57.582 33.333 0.00 0.00 34.08 1.28
133 134 9.322773 CATCTACTCCATATTATGATCGCATTT 57.677 33.333 5.21 0.00 35.94 2.32
139 140 8.311395 TGGTCCATCTACTCCATATTATGATC 57.689 38.462 5.21 0.00 0.00 2.92
153 154 3.243907 CGAATCCTTCCTGGTCCATCTAC 60.244 52.174 0.00 0.00 37.07 2.59
160 161 1.825474 TCACTCGAATCCTTCCTGGTC 59.175 52.381 0.00 0.00 37.07 4.02
162 163 2.432146 TGATCACTCGAATCCTTCCTGG 59.568 50.000 0.00 0.00 37.10 4.45
202 205 1.408822 GGGAACATGTGGGGTCATCTC 60.409 57.143 0.00 0.00 0.00 2.75
224 227 3.721087 AACATAAGTGGTCCAGGAAGG 57.279 47.619 0.00 0.00 39.47 3.46
231 234 6.127980 GGAGAAAAGCTTAACATAAGTGGTCC 60.128 42.308 0.00 0.00 0.00 4.46
257 260 4.803426 GTGGCAGGGAGAGCGACG 62.803 72.222 0.00 0.00 31.32 5.12
280 283 3.319198 ACCTTGGCCACCGACGAT 61.319 61.111 3.88 0.00 0.00 3.73
350 353 1.890876 AGATCGAGACTCATCGGAGG 58.109 55.000 2.82 0.00 45.81 4.30
418 422 0.912486 AAAGAAGGGGATGTAGCGCT 59.088 50.000 17.26 17.26 0.00 5.92
419 423 1.300481 GAAAGAAGGGGATGTAGCGC 58.700 55.000 0.00 0.00 0.00 5.92
420 424 1.134788 ACGAAAGAAGGGGATGTAGCG 60.135 52.381 0.00 0.00 0.00 4.26
455 459 7.421530 TTTCGACTTTAAAGGTCAGATTCAG 57.578 36.000 19.14 3.61 33.73 3.02
483 487 4.785376 AGAAGATTCAATGTGGGGTAGACT 59.215 41.667 0.00 0.00 0.00 3.24
490 494 5.011090 TCGTCTAGAAGATTCAATGTGGG 57.989 43.478 4.07 0.00 0.00 4.61
598 602 6.380079 AGGATATGAAGATTGGGATACACC 57.620 41.667 0.00 0.00 39.74 4.16
621 625 1.976898 CTAGCGTTGGTGTGGGGTA 59.023 57.895 0.00 0.00 0.00 3.69
637 641 0.806868 CGTGTCGTAGAGTTGGGCTA 59.193 55.000 0.00 0.00 36.95 3.93
641 645 0.388134 CCCACGTGTCGTAGAGTTGG 60.388 60.000 15.65 0.00 38.32 3.77
715 720 7.541916 AGGACCCTAGCTAACAATATTAGAC 57.458 40.000 0.00 0.00 0.00 2.59
796 802 7.349598 AGGACCAAGAAAAGCATGTATTAGAT 58.650 34.615 0.00 0.00 0.00 1.98
833 840 8.779303 CCTTGTTTTCCCCATTTTTAATGTAAC 58.221 33.333 0.00 0.00 0.00 2.50
849 856 1.654023 CGCCCGGATCCTTGTTTTCC 61.654 60.000 10.75 0.00 0.00 3.13
870 877 7.836842 TCCTTCCTTATATGCTTTCAAAAACC 58.163 34.615 0.00 0.00 0.00 3.27
912 919 4.957954 ACAAGATGAATAATGTGGGCATGT 59.042 37.500 0.00 0.00 35.15 3.21
923 930 8.690203 TCTTCCTTTTGTCACAAGATGAATAA 57.310 30.769 0.07 0.00 39.72 1.40
926 933 6.122277 ACTCTTCCTTTTGTCACAAGATGAA 58.878 36.000 0.07 0.00 39.72 2.57
961 969 5.130975 TGGAGGCTTGCAATCTTAGATCTAA 59.869 40.000 14.42 14.42 0.00 2.10
987 995 2.291930 GGTTCCCATGGTGGTGGAAATA 60.292 50.000 11.73 0.00 42.02 1.40
1053 1061 1.320344 CGGTGTCCAGTAGGCAGCTA 61.320 60.000 0.00 0.00 37.32 3.32
1054 1062 2.650116 CGGTGTCCAGTAGGCAGCT 61.650 63.158 0.00 0.00 37.32 4.24
1134 1142 4.684724 TGTGTAGAGTATTCTTGGGGTCT 58.315 43.478 0.00 0.00 34.79 3.85
1157 1165 3.998672 GGTGTGGACGGAAGCGGA 61.999 66.667 0.00 0.00 0.00 5.54
1175 1183 6.091441 GGATGAATAGTCGAGCATAATCCAAC 59.909 42.308 12.00 0.00 32.93 3.77
1180 1188 5.482908 GTGGGATGAATAGTCGAGCATAAT 58.517 41.667 0.00 0.00 0.00 1.28
1215 1223 1.270147 ACGGTGTTCACTAGAAGGCAC 60.270 52.381 0.00 0.34 33.63 5.01
1216 1224 1.000506 GACGGTGTTCACTAGAAGGCA 59.999 52.381 0.00 0.00 33.63 4.75
1242 1250 0.105401 TATCCCTGCCATGGTACCGA 60.105 55.000 14.67 5.07 0.00 4.69
1429 1437 3.728373 GCGGGGTGGGGATGAGTT 61.728 66.667 0.00 0.00 0.00 3.01
1489 1497 2.282040 GCTTGCAGTGTCAGGGCT 60.282 61.111 0.00 0.00 0.00 5.19
1499 1507 2.703416 TGTACCTGATGAAGCTTGCAG 58.297 47.619 2.10 8.61 0.00 4.41
1502 1510 8.668510 ATTAGTTATGTACCTGATGAAGCTTG 57.331 34.615 2.10 0.00 0.00 4.01
1572 1580 2.203280 CCTTGGTGGCCGTCAACA 60.203 61.111 0.00 0.00 42.14 3.33
1575 1583 2.847234 AGTCCTTGGTGGCCGTCA 60.847 61.111 0.00 0.00 35.26 4.35
1594 1602 2.594303 CGCAGGAAGTGGTGGCAA 60.594 61.111 0.00 0.00 0.00 4.52
1632 1640 3.891366 TGATGAGCGGAGTCAATAGATCA 59.109 43.478 0.00 0.00 33.45 2.92
1639 1647 3.648528 CGATGATGAGCGGAGTCAA 57.351 52.632 0.00 0.00 0.00 3.18
1672 1680 7.286316 ACAACTTTTCTGAGAATCCAACTGAAT 59.714 33.333 0.00 0.00 0.00 2.57
1673 1681 6.603201 ACAACTTTTCTGAGAATCCAACTGAA 59.397 34.615 0.00 0.00 0.00 3.02
1688 1696 3.881220 TCCACGAGGAAACAACTTTTCT 58.119 40.909 0.00 0.00 42.23 2.52
1745 1753 1.967779 TGAAGACCTCCACACGATTCA 59.032 47.619 0.00 0.00 0.00 2.57
1782 1790 0.161658 CGCGCACTAGCATATTTCCG 59.838 55.000 8.75 0.00 42.27 4.30
1788 1796 0.454196 TCTTCACGCGCACTAGCATA 59.546 50.000 5.73 0.00 42.27 3.14
1794 1802 1.617755 CGATGTTCTTCACGCGCACT 61.618 55.000 5.73 0.00 0.00 4.40
1884 1892 4.156556 GTGAAGTAGATGCAATTGGCTTCA 59.843 41.667 7.72 15.29 46.25 3.02
1908 1916 2.271800 GATGGTGAACTTAGGCACTCG 58.728 52.381 7.27 0.00 41.75 4.18
1914 1922 4.641396 TGTCTGTTGATGGTGAACTTAGG 58.359 43.478 0.00 0.00 0.00 2.69
1929 1937 5.030147 TCCTTGAGGTGGTATATGTCTGTT 58.970 41.667 0.00 0.00 36.34 3.16
1932 1940 3.637229 CGTCCTTGAGGTGGTATATGTCT 59.363 47.826 0.00 0.00 36.34 3.41
1938 1946 1.006758 TCTCCGTCCTTGAGGTGGTAT 59.993 52.381 9.71 0.00 34.77 2.73
1939 1947 0.406750 TCTCCGTCCTTGAGGTGGTA 59.593 55.000 9.71 0.55 34.77 3.25
1973 1983 2.334946 CCACCGGCAACACTCATGG 61.335 63.158 0.00 0.00 0.00 3.66
2005 2015 1.102978 GCGGGCATGTTTAGGTTCAT 58.897 50.000 0.00 0.00 0.00 2.57
2034 2044 2.072298 GGATGCTCGGTCATAGAATGC 58.928 52.381 0.00 0.00 0.00 3.56
2038 2048 1.332195 CAGGGATGCTCGGTCATAGA 58.668 55.000 0.00 0.00 0.00 1.98
2049 2059 0.743097 GAAAGATGGTGCAGGGATGC 59.257 55.000 0.00 0.00 0.00 3.91
2065 2075 5.148502 AGTGTAGAGGGAGAGAAGTTGAAA 58.851 41.667 0.00 0.00 0.00 2.69
2070 2080 4.742012 TGAAAGTGTAGAGGGAGAGAAGT 58.258 43.478 0.00 0.00 0.00 3.01
2171 2517 1.873591 CCTCAAGAAGGTCACCAAACG 59.126 52.381 0.00 0.00 40.67 3.60
2269 2615 6.751888 GCATGACAGAAAAACAAAAGTACACT 59.248 34.615 0.00 0.00 0.00 3.55
2270 2616 6.751888 AGCATGACAGAAAAACAAAAGTACAC 59.248 34.615 0.00 0.00 0.00 2.90
2389 2743 5.912149 AAGCACCAGAATGAATCCCTATA 57.088 39.130 0.00 0.00 39.69 1.31
2400 2754 1.331214 CACCACCAAAGCACCAGAAT 58.669 50.000 0.00 0.00 0.00 2.40
2432 2786 5.707298 ACTTCTAAAACAGACATGGACATGG 59.293 40.000 15.94 2.00 42.91 3.66
2555 2909 9.646427 GCGGATTTAGAGAGATAATAGACAAAT 57.354 33.333 0.00 0.00 0.00 2.32
2630 2987 9.689976 CACTGAGATAATTGACATAAGTAGAGG 57.310 37.037 0.00 0.00 0.00 3.69
2637 2994 9.725019 AAGACAACACTGAGATAATTGACATAA 57.275 29.630 0.00 0.00 0.00 1.90
2696 3053 0.246360 GCCCAGGCCACAATACAAAC 59.754 55.000 5.01 0.00 34.56 2.93
2697 3054 1.247419 CGCCCAGGCCACAATACAAA 61.247 55.000 5.01 0.00 37.98 2.83
2707 3064 2.203209 CAACTATCCGCCCAGGCC 60.203 66.667 2.37 0.00 40.77 5.19
2715 3072 6.978343 TTTAGGATTTGACACAACTATCCG 57.022 37.500 0.00 0.00 39.75 4.18
2780 3137 5.543507 ATCCTGGACAGTAGATGAATCAC 57.456 43.478 0.00 0.00 0.00 3.06
2814 3171 7.697352 TTTTGTATTCGTGACTCTTCGTAAA 57.303 32.000 0.00 0.00 0.00 2.01
2818 3175 5.176958 ACCTTTTTGTATTCGTGACTCTTCG 59.823 40.000 0.00 0.00 0.00 3.79
2820 3177 6.937436 AACCTTTTTGTATTCGTGACTCTT 57.063 33.333 0.00 0.00 0.00 2.85
2910 3269 0.625849 CACTAGGCATGAGGGGGTTT 59.374 55.000 0.00 0.00 0.00 3.27
2913 3272 2.512896 GCACTAGGCATGAGGGGG 59.487 66.667 0.00 0.00 43.97 5.40
2978 3337 5.353394 TTGCCCCATCTTACTAACACTAG 57.647 43.478 0.00 0.00 0.00 2.57
2980 3339 4.862641 ATTGCCCCATCTTACTAACACT 57.137 40.909 0.00 0.00 0.00 3.55
2998 3358 6.203338 ACTTTTGGCTTTTGTGCAATCTATTG 59.797 34.615 0.00 0.00 40.66 1.90
3075 3435 2.493675 TGTGAGCTACTCCACAGTGATC 59.506 50.000 0.62 0.00 33.62 2.92
3084 3444 3.118261 TCCATTTCCATGTGAGCTACTCC 60.118 47.826 0.00 0.00 0.00 3.85
3093 3453 4.467082 TCCTTCCATTTCCATTTCCATGTG 59.533 41.667 0.00 0.00 0.00 3.21
3095 3455 4.442472 GCTCCTTCCATTTCCATTTCCATG 60.442 45.833 0.00 0.00 0.00 3.66
3097 3457 3.099141 GCTCCTTCCATTTCCATTTCCA 58.901 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.