Multiple sequence alignment - TraesCS1D01G038600

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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 TraesCS1D01G038600 chr1D 100.000 2870 0 0 1 2870 18609568 18612437 0.000000e+00 5301.0
1 TraesCS1D01G038600 chr1D 88.379 2573 196 30 328 2870 18577207 18579706 0.000000e+00 3000.0
2 TraesCS1D01G038600 chr1D 85.198 1966 230 30 555 2472 18686516 18688468 0.000000e+00 1962.0
3 TraesCS1D01G038600 chr1D 91.679 1334 79 12 318 1627 18589807 18591132 0.000000e+00 1820.0
4 TraesCS1D01G038600 chr1D 96.203 316 12 0 2555 2870 18683548 18683863 4.240000e-143 518.0
5 TraesCS1D01G038600 chr1D 84.530 181 15 8 2689 2859 18688523 18688700 1.770000e-37 167.0
6 TraesCS1D01G038600 chr1A 93.646 2581 131 15 318 2870 20435240 20437815 0.000000e+00 3827.0
7 TraesCS1D01G038600 chr1A 92.308 1417 96 8 604 2016 20537089 20538496 0.000000e+00 2001.0
8 TraesCS1D01G038600 chr1A 91.003 289 22 2 319 604 20536756 20537043 1.250000e-103 387.0
9 TraesCS1D01G038600 chr1B 91.847 1153 86 4 880 2025 27277166 27278317 0.000000e+00 1602.0
10 TraesCS1D01G038600 chr1B 85.590 576 66 12 318 883 27272243 27272811 3.190000e-164 588.0
11 TraesCS1D01G038600 chr1B 91.057 123 10 1 2571 2692 448532830 448532952 6.360000e-37 165.0
12 TraesCS1D01G038600 chr5A 94.872 156 7 1 163 318 563730470 563730624 2.860000e-60 243.0
13 TraesCS1D01G038600 chr5A 94.156 154 8 1 163 316 563729204 563729356 1.720000e-57 233.0
14 TraesCS1D01G038600 chr5A 95.370 108 5 0 2587 2694 536122144 536122037 3.800000e-39 172.0
15 TraesCS1D01G038600 chr2A 94.231 156 8 1 163 318 19238731 19238577 1.330000e-58 237.0
16 TraesCS1D01G038600 chr5D 93.860 114 7 0 2581 2694 352456394 352456281 3.800000e-39 172.0
17 TraesCS1D01G038600 chr2D 90.698 129 11 1 2566 2694 6669268 6669395 1.370000e-38 171.0
18 TraesCS1D01G038600 chr7B 88.806 134 14 1 2559 2692 3887398 3887530 2.290000e-36 163.0
19 TraesCS1D01G038600 chr2B 86.111 144 19 1 2550 2693 612672734 612672876 1.380000e-33 154.0
20 TraesCS1D01G038600 chr6B 94.286 70 4 0 55 124 34164345 34164414 1.090000e-19 108.0
21 TraesCS1D01G038600 chr7D 100.000 55 0 0 70 124 49448493 49448439 5.060000e-18 102.0
22 TraesCS1D01G038600 chr7D 96.491 57 2 0 68 124 49449717 49449661 8.470000e-16 95.3


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 TraesCS1D01G038600 chr1D 18609568 18612437 2869 False 5301.000000 5301 100.000000 1 2870 1 chr1D.!!$F3 2869
1 TraesCS1D01G038600 chr1D 18577207 18579706 2499 False 3000.000000 3000 88.379000 328 2870 1 chr1D.!!$F1 2542
2 TraesCS1D01G038600 chr1D 18589807 18591132 1325 False 1820.000000 1820 91.679000 318 1627 1 chr1D.!!$F2 1309
3 TraesCS1D01G038600 chr1D 18683548 18688700 5152 False 882.333333 1962 88.643667 555 2870 3 chr1D.!!$F4 2315
4 TraesCS1D01G038600 chr1A 20435240 20437815 2575 False 3827.000000 3827 93.646000 318 2870 1 chr1A.!!$F1 2552
5 TraesCS1D01G038600 chr1A 20536756 20538496 1740 False 1194.000000 2001 91.655500 319 2016 2 chr1A.!!$F2 1697
6 TraesCS1D01G038600 chr1B 27277166 27278317 1151 False 1602.000000 1602 91.847000 880 2025 1 chr1B.!!$F2 1145
7 TraesCS1D01G038600 chr1B 27272243 27272811 568 False 588.000000 588 85.590000 318 883 1 chr1B.!!$F1 565
8 TraesCS1D01G038600 chr5A 563729204 563730624 1420 False 238.000000 243 94.514000 163 318 2 chr5A.!!$F1 155

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
21 22 0.032678 AAGTCTCACAGCCTCACGTG 59.967 55.0 9.94 9.94 34.34 4.49 F
50 51 0.107654 ACGCCTAACCAGGAGCAATC 60.108 55.0 0.00 0.00 45.12 2.67 F
824 3296 0.240945 CACCATTGGCGTTTCTCCAC 59.759 55.0 1.54 0.00 32.45 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 4085 0.109342 CCCAACACTGCTCACCTTCT 59.891 55.0 0.00 0.0 0.0 2.85 R
1791 4269 2.416547 CGGCAGTGGTATGAAGAAACAG 59.583 50.0 0.00 0.0 0.0 3.16 R
2678 5228 0.697079 TGTGAGTACTCCCTCCGTCT 59.303 55.0 20.11 0.0 0.0 4.18 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
19 20 1.871080 AAAAGTCTCACAGCCTCACG 58.129 50.000 0.00 0.00 0.00 4.35
20 21 0.753262 AAAGTCTCACAGCCTCACGT 59.247 50.000 0.00 0.00 0.00 4.49
21 22 0.032678 AAGTCTCACAGCCTCACGTG 59.967 55.000 9.94 9.94 34.34 4.49
22 23 1.109920 AGTCTCACAGCCTCACGTGT 61.110 55.000 16.51 0.00 34.66 4.49
23 24 0.596577 GTCTCACAGCCTCACGTGTA 59.403 55.000 16.51 1.31 34.66 2.90
26 27 3.066900 GTCTCACAGCCTCACGTGTATAT 59.933 47.826 16.51 0.00 34.66 0.86
27 28 4.275196 GTCTCACAGCCTCACGTGTATATA 59.725 45.833 16.51 0.00 34.66 0.86
29 30 6.148976 GTCTCACAGCCTCACGTGTATATATA 59.851 42.308 16.51 0.00 34.66 0.86
30 31 6.148976 TCTCACAGCCTCACGTGTATATATAC 59.851 42.308 16.51 14.86 34.66 1.47
43 44 6.519679 TGTATATATACACGCCTAACCAGG 57.480 41.667 19.51 0.00 40.39 4.45
46 47 0.464452 ATACACGCCTAACCAGGAGC 59.536 55.000 0.00 0.00 45.12 4.70
48 49 1.003839 CACGCCTAACCAGGAGCAA 60.004 57.895 0.00 0.00 45.12 3.91
49 50 0.392998 CACGCCTAACCAGGAGCAAT 60.393 55.000 0.00 0.00 45.12 3.56
50 51 0.107654 ACGCCTAACCAGGAGCAATC 60.108 55.000 0.00 0.00 45.12 2.67
51 52 0.815615 CGCCTAACCAGGAGCAATCC 60.816 60.000 0.00 0.00 45.91 3.01
52 53 0.548510 GCCTAACCAGGAGCAATCCT 59.451 55.000 0.00 0.00 45.91 3.24
56 57 2.808906 AACCAGGAGCAATCCTAACC 57.191 50.000 0.00 0.00 38.22 2.85
57 58 1.668826 ACCAGGAGCAATCCTAACCA 58.331 50.000 0.00 0.00 38.22 3.67
59 60 2.378547 ACCAGGAGCAATCCTAACCAAA 59.621 45.455 0.00 0.00 38.22 3.28
60 61 3.019564 CCAGGAGCAATCCTAACCAAAG 58.980 50.000 0.00 0.00 38.22 2.77
61 62 2.424956 CAGGAGCAATCCTAACCAAAGC 59.575 50.000 0.00 0.00 38.22 3.51
62 63 1.751351 GGAGCAATCCTAACCAAAGCC 59.249 52.381 0.00 0.00 0.00 4.35
63 64 2.621668 GGAGCAATCCTAACCAAAGCCT 60.622 50.000 0.00 0.00 0.00 4.58
65 66 3.621558 AGCAATCCTAACCAAAGCCTAC 58.378 45.455 0.00 0.00 0.00 3.18
67 68 4.017126 GCAATCCTAACCAAAGCCTACTT 58.983 43.478 0.00 0.00 37.90 2.24
68 69 4.142381 GCAATCCTAACCAAAGCCTACTTG 60.142 45.833 0.00 0.00 35.85 3.16
70 71 3.253220 TCCTAACCAAAGCCTACTTGGA 58.747 45.455 8.54 0.00 35.85 3.53
71 72 3.008704 TCCTAACCAAAGCCTACTTGGAC 59.991 47.826 8.54 0.00 35.85 4.02
72 73 3.009143 CCTAACCAAAGCCTACTTGGACT 59.991 47.826 8.54 0.00 35.85 3.85
73 74 2.861147 ACCAAAGCCTACTTGGACTC 57.139 50.000 8.54 0.00 35.85 3.36
74 75 1.002087 ACCAAAGCCTACTTGGACTCG 59.998 52.381 8.54 0.00 35.85 4.18
75 76 1.676014 CCAAAGCCTACTTGGACTCGG 60.676 57.143 0.00 0.00 35.85 4.63
77 78 1.900545 AAGCCTACTTGGACTCGGCC 61.901 60.000 0.00 0.00 41.60 6.13
81 82 1.829222 CCTACTTGGACTCGGCCTAAA 59.171 52.381 0.00 0.00 38.35 1.85
82 83 2.418334 CCTACTTGGACTCGGCCTAAAC 60.418 54.545 0.00 0.00 38.35 2.01
83 84 1.349067 ACTTGGACTCGGCCTAAACT 58.651 50.000 0.00 0.00 0.00 2.66
86 87 3.325716 ACTTGGACTCGGCCTAAACTAAA 59.674 43.478 0.00 0.00 0.00 1.85
87 88 3.323751 TGGACTCGGCCTAAACTAAAC 57.676 47.619 0.00 0.00 0.00 2.01
89 90 2.235650 GGACTCGGCCTAAACTAAACCT 59.764 50.000 0.00 0.00 0.00 3.50
90 91 3.448660 GGACTCGGCCTAAACTAAACCTA 59.551 47.826 0.00 0.00 0.00 3.08
91 92 4.100653 GGACTCGGCCTAAACTAAACCTAT 59.899 45.833 0.00 0.00 0.00 2.57
93 94 6.154203 ACTCGGCCTAAACTAAACCTATAC 57.846 41.667 0.00 0.00 0.00 1.47
95 96 4.037923 TCGGCCTAAACTAAACCTATACGG 59.962 45.833 0.00 0.00 39.35 4.02
96 97 4.060900 GGCCTAAACTAAACCTATACGGC 58.939 47.826 0.00 0.00 35.61 5.68
98 99 5.011023 GGCCTAAACTAAACCTATACGGCTA 59.989 44.000 0.00 0.00 35.61 3.93
100 101 6.986231 GCCTAAACTAAACCTATACGGCTAAA 59.014 38.462 0.00 0.00 35.61 1.85
103 104 9.591792 CTAAACTAAACCTATACGGCTAAACTT 57.408 33.333 0.00 0.00 35.61 2.66
105 106 6.577103 ACTAAACCTATACGGCTAAACTTCC 58.423 40.000 0.00 0.00 35.61 3.46
107 108 6.796785 AAACCTATACGGCTAAACTTCCTA 57.203 37.500 0.00 0.00 35.61 2.94
110 111 8.482852 AACCTATACGGCTAAACTTCCTAATA 57.517 34.615 0.00 0.00 35.61 0.98
111 112 7.890515 ACCTATACGGCTAAACTTCCTAATAC 58.109 38.462 0.00 0.00 35.61 1.89
113 114 8.362639 CCTATACGGCTAAACTTCCTAATACAA 58.637 37.037 0.00 0.00 0.00 2.41
116 117 7.748691 ACGGCTAAACTTCCTAATACAAAAA 57.251 32.000 0.00 0.00 0.00 1.94
117 118 7.587629 ACGGCTAAACTTCCTAATACAAAAAC 58.412 34.615 0.00 0.00 0.00 2.43
118 119 7.446319 ACGGCTAAACTTCCTAATACAAAAACT 59.554 33.333 0.00 0.00 0.00 2.66
119 120 8.938906 CGGCTAAACTTCCTAATACAAAAACTA 58.061 33.333 0.00 0.00 0.00 2.24
130 131 9.074576 CCTAATACAAAAACTAAACCTGAACCT 57.925 33.333 0.00 0.00 0.00 3.50
134 135 7.563888 ACAAAAACTAAACCTGAACCTAGAC 57.436 36.000 0.00 0.00 0.00 2.59
136 137 4.532314 AACTAAACCTGAACCTAGACGG 57.468 45.455 0.00 0.00 39.35 4.79
144 145 3.318017 CTGAACCTAGACGGACACAAAG 58.682 50.000 0.00 0.00 36.31 2.77
145 146 2.696707 TGAACCTAGACGGACACAAAGT 59.303 45.455 0.00 0.00 36.31 2.66
146 147 3.243636 TGAACCTAGACGGACACAAAGTC 60.244 47.826 0.00 0.00 46.83 3.01
159 160 5.140747 ACACAAAGTCCTACTTCTAGCTG 57.859 43.478 0.00 0.00 37.47 4.24
161 162 4.220821 CACAAAGTCCTACTTCTAGCTGGA 59.779 45.833 0.00 0.00 37.47 3.86
177 1281 4.317488 AGCTGGACTATACTACTACTCGC 58.683 47.826 0.00 0.00 0.00 5.03
238 1342 2.032620 CTCCTATACCACCAGCTCGTT 58.967 52.381 0.00 0.00 0.00 3.85
290 1394 0.478072 ATGTGCCAGGACTTGACCAA 59.522 50.000 0.00 0.00 0.00 3.67
378 1491 2.373502 CCAGAACAGAGGGTTTCTTCCT 59.626 50.000 0.00 0.00 40.63 3.36
492 1606 5.534654 TCCTACTTGTGTGGAAAAGATTTGG 59.465 40.000 0.00 0.00 0.00 3.28
501 1615 5.305128 TGTGGAAAAGATTTGGCTTTCTGAT 59.695 36.000 0.00 0.00 37.12 2.90
531 1645 6.219417 TCAGGCAAGAAACTTGAAATGAAA 57.781 33.333 14.44 0.00 0.00 2.69
606 3029 8.072567 GCATAATCACATTAGATTTGTGGTCTC 58.927 37.037 4.18 0.00 43.67 3.36
607 3030 9.334947 CATAATCACATTAGATTTGTGGTCTCT 57.665 33.333 4.18 0.00 43.67 3.10
610 3033 4.095483 CACATTAGATTTGTGGTCTCTGCC 59.905 45.833 0.00 0.00 40.60 4.85
634 3105 6.183360 CCTCTGATCTCGTTGTGGTAATCTTA 60.183 42.308 0.00 0.00 0.00 2.10
639 3110 8.204160 TGATCTCGTTGTGGTAATCTTATGATT 58.796 33.333 8.71 8.71 44.32 2.57
661 3133 7.882791 TGATTCAAGCCTGACAAGTATTCTTTA 59.117 33.333 0.00 0.00 0.00 1.85
697 3169 0.944386 GTCGTTTGCCAAGAAGCTGA 59.056 50.000 0.00 0.00 0.00 4.26
709 3181 4.318332 CAAGAAGCTGAAGACACACCATA 58.682 43.478 0.00 0.00 0.00 2.74
824 3296 0.240945 CACCATTGGCGTTTCTCCAC 59.759 55.000 1.54 0.00 32.45 4.02
845 3317 0.609957 CAAGAGCATTGCCTGACCCA 60.610 55.000 4.70 0.00 0.00 4.51
905 3377 1.756430 GTCTTTCCCCATGGAGAAGC 58.244 55.000 15.22 2.48 43.07 3.86
1073 3545 0.524862 CTTGTGGATGAGCCTGTTGC 59.475 55.000 0.00 0.00 41.71 4.17
1211 3686 2.962421 TCGTTGAAATTGGGCCTCTTTT 59.038 40.909 4.53 1.56 0.00 2.27
1607 4085 1.618837 CTTCCAGTCTCGAAGTTGGGA 59.381 52.381 8.40 0.44 33.50 4.37
1628 4106 2.282462 GGTGAGCAGTGTTGGGGG 60.282 66.667 0.00 0.00 0.00 5.40
1791 4269 5.164051 CGTATATGACATGCGAGATGGAAAC 60.164 44.000 0.00 0.00 0.00 2.78
2032 4559 1.000060 CATGTTGCAACTGGAAGGGTG 60.000 52.381 28.61 11.34 39.30 4.61
2035 4562 1.067060 GTTGCAACTGGAAGGGTGTTC 59.933 52.381 22.36 0.00 39.30 3.18
2203 4737 1.355381 TCTTGGTACGGGTCTGTAGGA 59.645 52.381 0.00 0.00 0.00 2.94
2298 4832 4.603989 TTCTTTCCAGAATTGCATTGCA 57.396 36.364 7.38 7.38 33.80 4.08
2427 4975 6.259550 AGTATGTCTTTGGTGCTCAAATTC 57.740 37.500 6.32 4.49 43.57 2.17
2536 5086 2.215196 GTGTAGGCACCGTCTTTGAAA 58.785 47.619 0.00 0.00 39.61 2.69
2584 5134 8.317679 GGATCTACATTGATAAGTATTGCCTCT 58.682 37.037 0.00 0.00 0.00 3.69
2607 5157 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
2620 5170 8.801882 ACTTGTCGGAGAAATGGATAAAAATA 57.198 30.769 0.00 0.00 39.69 1.40
2678 5228 9.695526 CATCCATTTCTTTGACAAGTATTTTCA 57.304 29.630 0.00 0.00 0.00 2.69
2681 5231 9.185192 CCATTTCTTTGACAAGTATTTTCAGAC 57.815 33.333 0.00 0.00 0.00 3.51
2831 5390 6.722590 TGAATTCATTTATATGGGATGCTGCT 59.277 34.615 3.38 0.00 32.40 4.24
2853 5412 5.042463 TCAACTGTTAATGTCTCCCAACA 57.958 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.139058 ACGTGAGGCTGTGAGACTTTT 59.861 47.619 0.00 0.00 30.20 2.27
1 2 0.753262 ACGTGAGGCTGTGAGACTTT 59.247 50.000 0.00 0.00 30.20 2.66
6 7 3.717400 ATATACACGTGAGGCTGTGAG 57.283 47.619 25.01 0.00 39.38 3.51
19 20 6.327934 CCTGGTTAGGCGTGTATATATACAC 58.672 44.000 32.71 32.71 44.94 2.90
20 21 6.247676 TCCTGGTTAGGCGTGTATATATACA 58.752 40.000 19.51 19.51 44.22 2.29
21 22 6.679884 GCTCCTGGTTAGGCGTGTATATATAC 60.680 46.154 14.86 14.86 44.22 1.47
22 23 5.359009 GCTCCTGGTTAGGCGTGTATATATA 59.641 44.000 0.00 0.00 44.22 0.86
23 24 4.159879 GCTCCTGGTTAGGCGTGTATATAT 59.840 45.833 0.00 0.00 44.22 0.86
26 27 1.684983 GCTCCTGGTTAGGCGTGTATA 59.315 52.381 0.00 0.00 44.22 1.47
27 28 0.464452 GCTCCTGGTTAGGCGTGTAT 59.536 55.000 0.00 0.00 44.22 2.29
29 30 1.764571 TTGCTCCTGGTTAGGCGTGT 61.765 55.000 0.00 0.00 44.22 4.49
30 31 0.392998 ATTGCTCCTGGTTAGGCGTG 60.393 55.000 0.00 0.00 44.22 5.34
32 33 0.815615 GGATTGCTCCTGGTTAGGCG 60.816 60.000 0.00 0.00 44.22 5.52
33 34 3.102090 GGATTGCTCCTGGTTAGGC 57.898 57.895 0.00 0.00 44.22 3.93
42 43 1.751351 GGCTTTGGTTAGGATTGCTCC 59.249 52.381 0.00 0.00 42.43 4.70
43 44 2.728007 AGGCTTTGGTTAGGATTGCTC 58.272 47.619 0.00 0.00 0.00 4.26
46 47 4.399303 CCAAGTAGGCTTTGGTTAGGATTG 59.601 45.833 9.40 0.00 31.49 2.67
48 49 3.850173 TCCAAGTAGGCTTTGGTTAGGAT 59.150 43.478 15.72 0.00 37.29 3.24
49 50 3.008704 GTCCAAGTAGGCTTTGGTTAGGA 59.991 47.826 15.72 2.50 37.29 2.94
50 51 3.009143 AGTCCAAGTAGGCTTTGGTTAGG 59.991 47.826 15.72 0.31 37.29 2.69
51 52 4.254492 GAGTCCAAGTAGGCTTTGGTTAG 58.746 47.826 15.72 0.00 37.29 2.34
52 53 3.306502 CGAGTCCAAGTAGGCTTTGGTTA 60.307 47.826 15.72 0.00 37.29 2.85
56 57 1.726853 CCGAGTCCAAGTAGGCTTTG 58.273 55.000 0.00 0.00 37.29 2.77
57 58 0.036294 GCCGAGTCCAAGTAGGCTTT 60.036 55.000 0.00 0.00 44.06 3.51
59 60 2.359967 GGCCGAGTCCAAGTAGGCT 61.360 63.158 4.73 0.00 46.44 4.58
60 61 1.041447 TAGGCCGAGTCCAAGTAGGC 61.041 60.000 0.00 0.00 46.51 3.93
61 62 1.481871 TTAGGCCGAGTCCAAGTAGG 58.518 55.000 0.00 0.00 39.47 3.18
62 63 2.496470 AGTTTAGGCCGAGTCCAAGTAG 59.504 50.000 0.00 0.00 0.00 2.57
63 64 2.532843 AGTTTAGGCCGAGTCCAAGTA 58.467 47.619 0.00 0.00 0.00 2.24
65 66 3.604875 TTAGTTTAGGCCGAGTCCAAG 57.395 47.619 0.00 0.00 0.00 3.61
67 68 2.027837 GGTTTAGTTTAGGCCGAGTCCA 60.028 50.000 0.00 0.00 0.00 4.02
68 69 2.235650 AGGTTTAGTTTAGGCCGAGTCC 59.764 50.000 0.00 0.00 0.00 3.85
70 71 5.221126 CGTATAGGTTTAGTTTAGGCCGAGT 60.221 44.000 0.00 0.00 0.00 4.18
71 72 5.218139 CGTATAGGTTTAGTTTAGGCCGAG 58.782 45.833 0.00 0.00 0.00 4.63
72 73 4.037923 CCGTATAGGTTTAGTTTAGGCCGA 59.962 45.833 0.00 0.00 34.51 5.54
73 74 4.301628 CCGTATAGGTTTAGTTTAGGCCG 58.698 47.826 0.00 0.00 34.51 6.13
74 75 4.060900 GCCGTATAGGTTTAGTTTAGGCC 58.939 47.826 0.00 0.00 43.70 5.19
75 76 4.953667 AGCCGTATAGGTTTAGTTTAGGC 58.046 43.478 0.00 0.00 43.70 3.93
77 78 9.591792 AAGTTTAGCCGTATAGGTTTAGTTTAG 57.408 33.333 0.00 0.00 43.70 1.85
81 82 6.382282 AGGAAGTTTAGCCGTATAGGTTTAGT 59.618 38.462 0.00 0.00 43.70 2.24
82 83 6.814043 AGGAAGTTTAGCCGTATAGGTTTAG 58.186 40.000 0.00 0.00 43.70 1.85
83 84 6.796785 AGGAAGTTTAGCCGTATAGGTTTA 57.203 37.500 0.00 0.00 43.70 2.01
86 87 6.990908 ATTAGGAAGTTTAGCCGTATAGGT 57.009 37.500 0.00 0.00 43.70 3.08
87 88 7.889469 TGTATTAGGAAGTTTAGCCGTATAGG 58.111 38.462 0.00 0.00 44.97 2.57
90 91 9.452287 TTTTTGTATTAGGAAGTTTAGCCGTAT 57.548 29.630 0.00 0.00 0.00 3.06
91 92 8.720562 GTTTTTGTATTAGGAAGTTTAGCCGTA 58.279 33.333 0.00 0.00 0.00 4.02
93 94 7.813645 AGTTTTTGTATTAGGAAGTTTAGCCG 58.186 34.615 0.00 0.00 0.00 5.52
100 101 9.856162 TCAGGTTTAGTTTTTGTATTAGGAAGT 57.144 29.630 0.00 0.00 0.00 3.01
103 104 9.070179 GGTTCAGGTTTAGTTTTTGTATTAGGA 57.930 33.333 0.00 0.00 0.00 2.94
107 108 9.856162 TCTAGGTTCAGGTTTAGTTTTTGTATT 57.144 29.630 0.00 0.00 0.00 1.89
110 111 6.259387 CGTCTAGGTTCAGGTTTAGTTTTTGT 59.741 38.462 0.00 0.00 0.00 2.83
111 112 6.293244 CCGTCTAGGTTCAGGTTTAGTTTTTG 60.293 42.308 0.00 0.00 34.51 2.44
113 114 5.070847 TCCGTCTAGGTTCAGGTTTAGTTTT 59.929 40.000 0.00 0.00 41.99 2.43
116 117 3.509184 GTCCGTCTAGGTTCAGGTTTAGT 59.491 47.826 0.00 0.00 41.99 2.24
117 118 3.508793 TGTCCGTCTAGGTTCAGGTTTAG 59.491 47.826 0.00 0.00 41.99 1.85
118 119 3.256631 GTGTCCGTCTAGGTTCAGGTTTA 59.743 47.826 0.00 0.00 41.99 2.01
119 120 2.036862 GTGTCCGTCTAGGTTCAGGTTT 59.963 50.000 0.00 0.00 41.99 3.27
120 121 1.617357 GTGTCCGTCTAGGTTCAGGTT 59.383 52.381 0.00 0.00 41.99 3.50
121 122 1.254954 GTGTCCGTCTAGGTTCAGGT 58.745 55.000 0.00 0.00 41.99 4.00
122 123 1.254026 TGTGTCCGTCTAGGTTCAGG 58.746 55.000 0.00 0.00 41.99 3.86
124 125 2.696707 ACTTTGTGTCCGTCTAGGTTCA 59.303 45.455 0.00 0.00 41.99 3.18
136 137 5.164954 CAGCTAGAAGTAGGACTTTGTGTC 58.835 45.833 0.00 0.00 38.80 3.67
145 146 6.766997 AGTATAGTCCAGCTAGAAGTAGGA 57.233 41.667 0.00 0.00 32.45 2.94
146 147 7.682628 AGTAGTATAGTCCAGCTAGAAGTAGG 58.317 42.308 0.00 0.00 32.45 3.18
149 150 8.266363 AGTAGTAGTATAGTCCAGCTAGAAGT 57.734 38.462 0.00 0.00 32.45 3.01
150 151 7.543172 CGAGTAGTAGTATAGTCCAGCTAGAAG 59.457 44.444 0.00 0.00 32.45 2.85
151 152 7.377398 CGAGTAGTAGTATAGTCCAGCTAGAA 58.623 42.308 0.00 0.00 32.45 2.10
152 153 6.572119 GCGAGTAGTAGTATAGTCCAGCTAGA 60.572 46.154 0.00 0.00 32.45 2.43
153 154 5.577945 GCGAGTAGTAGTATAGTCCAGCTAG 59.422 48.000 0.00 0.00 32.45 3.42
156 157 3.123284 CGCGAGTAGTAGTATAGTCCAGC 59.877 52.174 0.00 0.00 0.00 4.85
238 1342 7.171630 GGATAGTTTCCTAGTTGAGTCAAGA 57.828 40.000 5.62 0.00 41.78 3.02
501 1615 0.874390 GTTTCTTGCCTGATGCGTCA 59.126 50.000 8.64 8.64 45.60 4.35
531 1645 9.933240 AGGAAATCATCAATAGGATTCTCTTTT 57.067 29.630 0.00 0.00 35.14 2.27
606 3029 1.638133 CACAACGAGATCAGAGGCAG 58.362 55.000 0.00 0.00 0.00 4.85
607 3030 0.247460 CCACAACGAGATCAGAGGCA 59.753 55.000 0.00 0.00 0.00 4.75
610 3033 5.255710 AGATTACCACAACGAGATCAGAG 57.744 43.478 0.00 0.00 0.00 3.35
634 3105 6.421485 AGAATACTTGTCAGGCTTGAATCAT 58.579 36.000 0.00 0.00 34.49 2.45
639 3110 6.769512 AGTAAAGAATACTTGTCAGGCTTGA 58.230 36.000 0.00 0.00 36.39 3.02
697 3169 4.701651 CCATGATTGTGTATGGTGTGTCTT 59.298 41.667 0.00 0.00 39.18 3.01
709 3181 0.700564 AGGGCTGACCATGATTGTGT 59.299 50.000 0.47 0.00 43.89 3.72
824 3296 0.524862 GGTCAGGCAATGCTCTTGTG 59.475 55.000 4.82 0.00 0.00 3.33
845 3317 2.008242 TGCAAGCCATGGTAAAGGTT 57.992 45.000 14.67 0.00 0.00 3.50
1073 3545 7.355017 CAGGACATCACGACCATTAATAATTG 58.645 38.462 0.00 0.00 30.94 2.32
1114 3589 2.532250 TCCATCTGTAGCAGAGGACA 57.468 50.000 11.68 0.00 43.80 4.02
1211 3686 0.179070 TTGGCAGTACGCAACAGTGA 60.179 50.000 0.00 0.00 45.17 3.41
1607 4085 0.109342 CCCAACACTGCTCACCTTCT 59.891 55.000 0.00 0.00 0.00 2.85
1628 4106 2.476619 CTGACGAACAATGTCTGGTCAC 59.523 50.000 9.13 0.00 42.46 3.67
1791 4269 2.416547 CGGCAGTGGTATGAAGAAACAG 59.583 50.000 0.00 0.00 0.00 3.16
2203 4737 7.499232 GCAAGAAGGTACTGTAAATATGATGGT 59.501 37.037 0.00 0.00 40.86 3.55
2298 4832 9.135189 ACCAAGACATGCATTGTTTATATACAT 57.865 29.630 0.00 0.00 39.18 2.29
2454 5004 0.899720 ATTGCCTTGGTGCCAGATTG 59.100 50.000 0.00 0.00 0.00 2.67
2495 5045 7.817418 ACACAAAGTAATGTTACAAGGTGAT 57.183 32.000 18.73 7.94 35.48 3.06
2536 5086 5.076318 TCCTGAATTATAGAATGGGGGCATT 59.924 40.000 0.00 0.00 0.00 3.56
2577 5127 1.906574 AGTATTTCCGGACAGAGGCAA 59.093 47.619 1.83 0.00 0.00 4.52
2584 5134 1.894466 TCCGACAAGTATTTCCGGACA 59.106 47.619 1.83 0.00 43.47 4.02
2664 5214 4.562757 CCCTCCGTCTGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2678 5228 0.697079 TGTGAGTACTCCCTCCGTCT 59.303 55.000 20.11 0.00 0.00 4.18
2681 5231 1.473278 GACTTGTGAGTACTCCCTCCG 59.527 57.143 20.11 7.45 35.88 4.63
2784 5343 4.616802 CAGATTTCGCATGGTTTGTACAAC 59.383 41.667 8.07 3.81 0.00 3.32
2831 5390 5.042463 TGTTGGGAGACATTAACAGTTGA 57.958 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.