Multiple sequence alignment - TraesCS4A01G355900

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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 TraesCS4A01G355900 chr4A 100.000 3044 0 0 1 3044 629488331 629485288 0.000000e+00 5622
1 TraesCS4A01G355900 chr5D 92.993 2954 102 36 141 3044 539013482 539016380 0.000000e+00 4211
2 TraesCS4A01G355900 chr5D 78.619 449 75 16 1190 1637 410241859 410241431 8.310000e-71 278
3 TraesCS4A01G355900 chr5B 92.376 2361 90 35 141 2458 680579492 680581805 0.000000e+00 3280
4 TraesCS4A01G355900 chr5B 89.549 488 36 9 2558 3044 680581838 680582311 3.360000e-169 604
5 TraesCS4A01G355900 chr5B 79.780 455 74 14 1190 1637 491994863 491994420 6.340000e-82 315
6 TraesCS4A01G355900 chr2D 95.122 451 15 5 995 1444 520537211 520536767 0.000000e+00 704
7 TraesCS4A01G355900 chr4B 93.080 289 18 1 2756 3044 584072879 584073165 3.630000e-114 422
8 TraesCS4A01G355900 chr5A 80.250 400 62 13 1190 1582 521744636 521744247 4.970000e-73 285
9 TraesCS4A01G355900 chr5A 89.583 96 9 1 1 95 534265609 534265704 1.480000e-23 121
10 TraesCS4A01G355900 chr1B 88.360 189 21 1 1451 1638 460487613 460487425 3.050000e-55 226


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 TraesCS4A01G355900 chr4A 629485288 629488331 3043 True 5622 5622 100.0000 1 3044 1 chr4A.!!$R1 3043
1 TraesCS4A01G355900 chr5D 539013482 539016380 2898 False 4211 4211 92.9930 141 3044 1 chr5D.!!$F1 2903
2 TraesCS4A01G355900 chr5B 680579492 680582311 2819 False 1942 3280 90.9625 141 3044 2 chr5B.!!$F1 2903

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
116 117 0.031994 CGAAACCCCTTTGCCACAAG 59.968 55.000 0.0 0.0 0.0 3.16 F
117 118 1.119684 GAAACCCCTTTGCCACAAGT 58.880 50.000 0.0 0.0 0.0 3.16 F
431 458 1.135112 GGTGCCTTTTTATTCCAGCGG 60.135 52.381 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1493 4.144727 GGAGGAGGCGGAGGAGGA 62.145 72.222 0.00 0.0 0.0 3.71 R
1776 1837 4.243008 TGTGGCGCGGACTGGAAA 62.243 61.111 8.83 0.0 0.0 3.13 R
2384 2463 0.884704 TTCAAGCTGGTGTTCGCCTC 60.885 55.000 4.05 0.0 0.0 4.70 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
39 40 8.806177 GGTACCAATTTCAAGAATTTAAACGT 57.194 30.769 7.15 0.00 0.00 3.99
40 41 8.696175 GGTACCAATTTCAAGAATTTAAACGTG 58.304 33.333 7.15 0.00 0.00 4.49
41 42 9.453325 GTACCAATTTCAAGAATTTAAACGTGA 57.547 29.630 0.00 0.00 0.00 4.35
42 43 8.574196 ACCAATTTCAAGAATTTAAACGTGAG 57.426 30.769 0.00 0.00 0.00 3.51
43 44 7.651704 ACCAATTTCAAGAATTTAAACGTGAGG 59.348 33.333 0.00 0.00 0.00 3.86
44 45 7.865385 CCAATTTCAAGAATTTAAACGTGAGGA 59.135 33.333 0.00 0.00 0.00 3.71
45 46 9.410556 CAATTTCAAGAATTTAAACGTGAGGAT 57.589 29.630 0.00 0.00 0.00 3.24
46 47 9.981114 AATTTCAAGAATTTAAACGTGAGGATT 57.019 25.926 0.00 0.00 0.00 3.01
47 48 9.626045 ATTTCAAGAATTTAAACGTGAGGATTC 57.374 29.630 0.00 0.00 0.00 2.52
48 49 7.737972 TCAAGAATTTAAACGTGAGGATTCA 57.262 32.000 13.79 0.00 0.00 2.57
49 50 8.335532 TCAAGAATTTAAACGTGAGGATTCAT 57.664 30.769 13.79 3.59 35.39 2.57
50 51 8.792633 TCAAGAATTTAAACGTGAGGATTCATT 58.207 29.630 13.79 6.12 35.39 2.57
51 52 9.410556 CAAGAATTTAAACGTGAGGATTCATTT 57.589 29.630 13.79 2.72 35.39 2.32
52 53 8.970691 AGAATTTAAACGTGAGGATTCATTTG 57.029 30.769 13.79 0.00 35.39 2.32
53 54 7.542130 AGAATTTAAACGTGAGGATTCATTTGC 59.458 33.333 13.79 0.00 35.39 3.68
54 55 2.900122 AACGTGAGGATTCATTTGCG 57.100 45.000 0.00 0.00 35.39 4.85
55 56 1.808411 ACGTGAGGATTCATTTGCGT 58.192 45.000 0.00 0.00 35.39 5.24
56 57 1.732259 ACGTGAGGATTCATTTGCGTC 59.268 47.619 0.00 0.00 35.39 5.19
57 58 1.731709 CGTGAGGATTCATTTGCGTCA 59.268 47.619 0.00 0.00 35.39 4.35
58 59 2.474526 CGTGAGGATTCATTTGCGTCAC 60.475 50.000 0.00 0.00 41.45 3.67
59 60 1.731709 TGAGGATTCATTTGCGTCACG 59.268 47.619 0.00 0.00 0.00 4.35
76 77 5.759963 CGTCACGCTCTATAATCTTAAGGT 58.240 41.667 1.85 0.00 0.00 3.50
77 78 6.207213 CGTCACGCTCTATAATCTTAAGGTT 58.793 40.000 6.19 6.19 0.00 3.50
78 79 6.360148 CGTCACGCTCTATAATCTTAAGGTTC 59.640 42.308 3.71 0.00 0.00 3.62
79 80 7.201145 GTCACGCTCTATAATCTTAAGGTTCA 58.799 38.462 3.71 0.00 0.00 3.18
80 81 7.705325 GTCACGCTCTATAATCTTAAGGTTCAA 59.295 37.037 3.71 0.00 0.00 2.69
81 82 8.255206 TCACGCTCTATAATCTTAAGGTTCAAA 58.745 33.333 3.71 0.00 0.00 2.69
82 83 8.879759 CACGCTCTATAATCTTAAGGTTCAAAA 58.120 33.333 3.71 0.00 0.00 2.44
83 84 8.880750 ACGCTCTATAATCTTAAGGTTCAAAAC 58.119 33.333 3.71 0.00 0.00 2.43
84 85 8.879759 CGCTCTATAATCTTAAGGTTCAAAACA 58.120 33.333 3.71 0.00 0.00 2.83
91 92 8.519799 AATCTTAAGGTTCAAAACAGACTTCA 57.480 30.769 1.85 0.00 0.00 3.02
92 93 7.316544 TCTTAAGGTTCAAAACAGACTTCAC 57.683 36.000 1.85 0.00 0.00 3.18
93 94 7.110155 TCTTAAGGTTCAAAACAGACTTCACT 58.890 34.615 1.85 0.00 0.00 3.41
94 95 5.819825 AAGGTTCAAAACAGACTTCACTC 57.180 39.130 0.00 0.00 0.00 3.51
95 96 3.871594 AGGTTCAAAACAGACTTCACTCG 59.128 43.478 0.00 0.00 0.00 4.18
96 97 3.621715 GGTTCAAAACAGACTTCACTCGT 59.378 43.478 0.00 0.00 0.00 4.18
97 98 4.260253 GGTTCAAAACAGACTTCACTCGTC 60.260 45.833 0.00 0.00 0.00 4.20
98 99 3.113322 TCAAAACAGACTTCACTCGTCG 58.887 45.455 0.00 0.00 36.53 5.12
99 100 3.113322 CAAAACAGACTTCACTCGTCGA 58.887 45.455 0.00 0.00 36.53 4.20
100 101 3.431922 AAACAGACTTCACTCGTCGAA 57.568 42.857 0.00 0.00 36.53 3.71
101 102 3.431922 AACAGACTTCACTCGTCGAAA 57.568 42.857 0.00 0.00 36.53 3.46
102 103 2.728922 ACAGACTTCACTCGTCGAAAC 58.271 47.619 0.00 0.00 36.53 2.78
103 104 2.052157 CAGACTTCACTCGTCGAAACC 58.948 52.381 0.00 0.00 36.53 3.27
104 105 1.000496 AGACTTCACTCGTCGAAACCC 60.000 52.381 0.00 0.00 36.53 4.11
105 106 0.033090 ACTTCACTCGTCGAAACCCC 59.967 55.000 0.00 0.00 0.00 4.95
106 107 0.317479 CTTCACTCGTCGAAACCCCT 59.683 55.000 0.00 0.00 0.00 4.79
107 108 0.754472 TTCACTCGTCGAAACCCCTT 59.246 50.000 0.00 0.00 0.00 3.95
108 109 0.754472 TCACTCGTCGAAACCCCTTT 59.246 50.000 0.00 0.00 0.00 3.11
109 110 0.865769 CACTCGTCGAAACCCCTTTG 59.134 55.000 0.00 0.00 0.00 2.77
110 111 0.883370 ACTCGTCGAAACCCCTTTGC 60.883 55.000 0.00 0.00 0.00 3.68
111 112 1.574702 CTCGTCGAAACCCCTTTGCC 61.575 60.000 0.00 0.00 0.00 4.52
112 113 1.894756 CGTCGAAACCCCTTTGCCA 60.895 57.895 0.00 0.00 0.00 4.92
113 114 1.658114 GTCGAAACCCCTTTGCCAC 59.342 57.895 0.00 0.00 0.00 5.01
114 115 1.104577 GTCGAAACCCCTTTGCCACA 61.105 55.000 0.00 0.00 0.00 4.17
115 116 0.395862 TCGAAACCCCTTTGCCACAA 60.396 50.000 0.00 0.00 0.00 3.33
116 117 0.031994 CGAAACCCCTTTGCCACAAG 59.968 55.000 0.00 0.00 0.00 3.16
117 118 1.119684 GAAACCCCTTTGCCACAAGT 58.880 50.000 0.00 0.00 0.00 3.16
118 119 1.484653 GAAACCCCTTTGCCACAAGTT 59.515 47.619 0.00 0.00 0.00 2.66
119 120 1.578897 AACCCCTTTGCCACAAGTTT 58.421 45.000 0.00 0.00 0.00 2.66
120 121 2.463047 ACCCCTTTGCCACAAGTTTA 57.537 45.000 0.00 0.00 0.00 2.01
121 122 2.970987 ACCCCTTTGCCACAAGTTTAT 58.029 42.857 0.00 0.00 0.00 1.40
122 123 3.313791 ACCCCTTTGCCACAAGTTTATT 58.686 40.909 0.00 0.00 0.00 1.40
123 124 3.714280 ACCCCTTTGCCACAAGTTTATTT 59.286 39.130 0.00 0.00 0.00 1.40
124 125 4.902448 ACCCCTTTGCCACAAGTTTATTTA 59.098 37.500 0.00 0.00 0.00 1.40
125 126 5.546110 ACCCCTTTGCCACAAGTTTATTTAT 59.454 36.000 0.00 0.00 0.00 1.40
126 127 6.726764 ACCCCTTTGCCACAAGTTTATTTATA 59.273 34.615 0.00 0.00 0.00 0.98
127 128 7.093509 ACCCCTTTGCCACAAGTTTATTTATAG 60.094 37.037 0.00 0.00 0.00 1.31
128 129 6.756542 CCCTTTGCCACAAGTTTATTTATAGC 59.243 38.462 0.00 0.00 0.00 2.97
129 130 6.756542 CCTTTGCCACAAGTTTATTTATAGCC 59.243 38.462 0.00 0.00 0.00 3.93
130 131 6.842437 TTGCCACAAGTTTATTTATAGCCA 57.158 33.333 0.00 0.00 0.00 4.75
131 132 6.842437 TGCCACAAGTTTATTTATAGCCAA 57.158 33.333 0.00 0.00 0.00 4.52
132 133 7.233389 TGCCACAAGTTTATTTATAGCCAAA 57.767 32.000 0.00 0.00 0.00 3.28
133 134 7.671302 TGCCACAAGTTTATTTATAGCCAAAA 58.329 30.769 0.00 0.00 0.00 2.44
134 135 8.150945 TGCCACAAGTTTATTTATAGCCAAAAA 58.849 29.630 0.00 0.00 0.00 1.94
194 202 3.764466 AGTGCCGAGCGGAAGGAG 61.764 66.667 13.94 0.00 37.50 3.69
329 346 4.329545 GCTGGGACCAACGCCAGA 62.330 66.667 8.49 0.00 38.40 3.86
345 362 4.767255 GACCAGCTGCCAGTCCCG 62.767 72.222 8.66 0.00 0.00 5.14
431 458 1.135112 GGTGCCTTTTTATTCCAGCGG 60.135 52.381 0.00 0.00 0.00 5.52
561 595 1.957668 ATCACGCGTTAATTACCCCC 58.042 50.000 10.22 0.00 0.00 5.40
710 751 2.742372 CAGGGGGAAACGACAGCG 60.742 66.667 0.00 0.00 44.79 5.18
1432 1493 2.042930 GGATCCCCACCCAGTCCT 59.957 66.667 0.00 0.00 0.00 3.85
1433 1494 2.073101 GGATCCCCACCCAGTCCTC 61.073 68.421 0.00 0.00 0.00 3.71
1434 1495 2.042930 ATCCCCACCCAGTCCTCC 59.957 66.667 0.00 0.00 0.00 4.30
1435 1496 2.553438 GATCCCCACCCAGTCCTCCT 62.553 65.000 0.00 0.00 0.00 3.69
1436 1497 2.553438 ATCCCCACCCAGTCCTCCTC 62.553 65.000 0.00 0.00 0.00 3.71
1437 1498 2.689034 CCCACCCAGTCCTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
1438 1499 2.452114 CCACCCAGTCCTCCTCCT 59.548 66.667 0.00 0.00 0.00 3.69
1439 1500 1.687493 CCACCCAGTCCTCCTCCTC 60.687 68.421 0.00 0.00 0.00 3.71
1440 1501 1.687493 CACCCAGTCCTCCTCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
1839 1900 4.479993 ATGCCGGCTGGAGCTGTC 62.480 66.667 29.70 0.00 45.66 3.51
1874 1935 1.421410 GCCGACTACCATCAACAGCG 61.421 60.000 0.00 0.00 0.00 5.18
2279 2346 6.391227 AGAACACGAAACATGGAGAAAAAT 57.609 33.333 0.00 0.00 0.00 1.82
2391 2470 0.543410 TGAACTACAGGGGAGGCGAA 60.543 55.000 0.00 0.00 0.00 4.70
2392 2471 0.108281 GAACTACAGGGGAGGCGAAC 60.108 60.000 0.00 0.00 0.00 3.95
2394 2473 1.218316 CTACAGGGGAGGCGAACAC 59.782 63.158 0.00 0.00 0.00 3.32
2458 2547 8.688747 ATGTATCTGAAGGAAATTGATCTTCC 57.311 34.615 4.42 4.42 42.40 3.46
2577 2667 7.951530 AATTCTTTTGATTTTCACATCGCTT 57.048 28.000 0.00 0.00 0.00 4.68
2618 2708 5.531634 TGGAATTTCATGAACAAGTTCTGC 58.468 37.500 7.89 0.89 40.14 4.26
2619 2709 4.925646 GGAATTTCATGAACAAGTTCTGCC 59.074 41.667 7.89 0.00 40.14 4.85
2620 2710 4.525912 ATTTCATGAACAAGTTCTGCCC 57.474 40.909 7.89 0.00 40.14 5.36
2622 2712 3.228188 TCATGAACAAGTTCTGCCCTT 57.772 42.857 13.49 0.00 40.14 3.95
2623 2713 3.565307 TCATGAACAAGTTCTGCCCTTT 58.435 40.909 13.49 0.00 40.14 3.11
2624 2714 3.318839 TCATGAACAAGTTCTGCCCTTTG 59.681 43.478 13.49 0.00 40.14 2.77
2625 2715 3.011566 TGAACAAGTTCTGCCCTTTGA 57.988 42.857 13.49 0.00 40.14 2.69
2626 2716 2.687935 TGAACAAGTTCTGCCCTTTGAC 59.312 45.455 13.49 0.00 40.14 3.18
2627 2717 1.692411 ACAAGTTCTGCCCTTTGACC 58.308 50.000 0.00 0.00 0.00 4.02
2628 2718 0.593128 CAAGTTCTGCCCTTTGACCG 59.407 55.000 0.00 0.00 0.00 4.79
2629 2719 0.472471 AAGTTCTGCCCTTTGACCGA 59.528 50.000 0.00 0.00 0.00 4.69
2630 2720 0.472471 AGTTCTGCCCTTTGACCGAA 59.528 50.000 0.00 0.00 0.00 4.30
2631 2721 1.073923 AGTTCTGCCCTTTGACCGAAT 59.926 47.619 0.00 0.00 0.00 3.34
2632 2722 1.886542 GTTCTGCCCTTTGACCGAATT 59.113 47.619 0.00 0.00 0.00 2.17
2633 2723 3.078837 GTTCTGCCCTTTGACCGAATTA 58.921 45.455 0.00 0.00 0.00 1.40
2634 2724 3.426787 TCTGCCCTTTGACCGAATTAA 57.573 42.857 0.00 0.00 0.00 1.40
2635 2725 3.963129 TCTGCCCTTTGACCGAATTAAT 58.037 40.909 0.00 0.00 0.00 1.40
2636 2726 4.340617 TCTGCCCTTTGACCGAATTAATT 58.659 39.130 0.00 0.00 0.00 1.40
2881 2973 3.838244 TGTTGCTACAGTCCTGTCTTT 57.162 42.857 2.65 0.00 43.74 2.52
3000 3100 2.421424 GGACCTGCACATAAAAGAGCTG 59.579 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.778059 TGAAATTGGTACCCTATACTTCTTGAT 58.222 33.333 10.07 0.00 0.00 2.57
1 2 8.153221 TGAAATTGGTACCCTATACTTCTTGA 57.847 34.615 10.07 0.00 0.00 3.02
2 3 8.801882 TTGAAATTGGTACCCTATACTTCTTG 57.198 34.615 10.07 0.00 0.00 3.02
3 4 8.832735 TCTTGAAATTGGTACCCTATACTTCTT 58.167 33.333 10.07 0.00 0.00 2.52
4 5 8.388656 TCTTGAAATTGGTACCCTATACTTCT 57.611 34.615 10.07 0.00 0.00 2.85
5 6 9.628500 ATTCTTGAAATTGGTACCCTATACTTC 57.372 33.333 10.07 5.68 0.00 3.01
6 7 9.990868 AATTCTTGAAATTGGTACCCTATACTT 57.009 29.630 10.07 0.00 0.00 2.24
7 8 9.990868 AAATTCTTGAAATTGGTACCCTATACT 57.009 29.630 10.07 0.00 0.00 2.12
12 13 8.085909 CGTTTAAATTCTTGAAATTGGTACCCT 58.914 33.333 10.07 0.00 0.00 4.34
13 14 7.868922 ACGTTTAAATTCTTGAAATTGGTACCC 59.131 33.333 10.07 0.00 0.00 3.69
14 15 8.696175 CACGTTTAAATTCTTGAAATTGGTACC 58.304 33.333 4.43 4.43 0.00 3.34
15 16 9.453325 TCACGTTTAAATTCTTGAAATTGGTAC 57.547 29.630 0.00 0.00 0.00 3.34
16 17 9.672086 CTCACGTTTAAATTCTTGAAATTGGTA 57.328 29.630 0.00 0.00 0.00 3.25
17 18 7.651704 CCTCACGTTTAAATTCTTGAAATTGGT 59.348 33.333 0.00 0.00 0.00 3.67
18 19 7.865385 TCCTCACGTTTAAATTCTTGAAATTGG 59.135 33.333 0.00 0.00 0.00 3.16
19 20 8.795786 TCCTCACGTTTAAATTCTTGAAATTG 57.204 30.769 0.00 0.00 0.00 2.32
20 21 9.981114 AATCCTCACGTTTAAATTCTTGAAATT 57.019 25.926 0.00 0.00 0.00 1.82
21 22 9.626045 GAATCCTCACGTTTAAATTCTTGAAAT 57.374 29.630 0.00 0.00 0.00 2.17
22 23 8.625651 TGAATCCTCACGTTTAAATTCTTGAAA 58.374 29.630 10.22 0.00 0.00 2.69
23 24 8.160521 TGAATCCTCACGTTTAAATTCTTGAA 57.839 30.769 10.22 0.00 0.00 2.69
24 25 7.737972 TGAATCCTCACGTTTAAATTCTTGA 57.262 32.000 10.22 0.00 0.00 3.02
25 26 8.970691 AATGAATCCTCACGTTTAAATTCTTG 57.029 30.769 10.22 0.00 33.30 3.02
26 27 9.410556 CAAATGAATCCTCACGTTTAAATTCTT 57.589 29.630 10.22 3.85 33.30 2.52
27 28 7.542130 GCAAATGAATCCTCACGTTTAAATTCT 59.458 33.333 10.22 0.00 33.30 2.40
28 29 7.461416 CGCAAATGAATCCTCACGTTTAAATTC 60.461 37.037 0.00 0.00 33.30 2.17
29 30 6.307800 CGCAAATGAATCCTCACGTTTAAATT 59.692 34.615 0.00 0.00 33.30 1.82
30 31 5.799936 CGCAAATGAATCCTCACGTTTAAAT 59.200 36.000 0.00 0.00 33.30 1.40
31 32 5.150683 CGCAAATGAATCCTCACGTTTAAA 58.849 37.500 0.00 0.00 33.30 1.52
32 33 4.214545 ACGCAAATGAATCCTCACGTTTAA 59.785 37.500 0.00 0.00 33.30 1.52
33 34 3.749088 ACGCAAATGAATCCTCACGTTTA 59.251 39.130 0.00 0.00 33.30 2.01
34 35 2.552315 ACGCAAATGAATCCTCACGTTT 59.448 40.909 0.00 0.00 33.30 3.60
35 36 2.151202 ACGCAAATGAATCCTCACGTT 58.849 42.857 0.00 0.00 33.30 3.99
36 37 1.732259 GACGCAAATGAATCCTCACGT 59.268 47.619 0.00 0.00 34.40 4.49
37 38 1.731709 TGACGCAAATGAATCCTCACG 59.268 47.619 0.00 0.00 33.30 4.35
38 39 2.474526 CGTGACGCAAATGAATCCTCAC 60.475 50.000 0.00 0.00 33.30 3.51
39 40 1.731709 CGTGACGCAAATGAATCCTCA 59.268 47.619 0.00 0.00 35.56 3.86
40 41 2.442189 CGTGACGCAAATGAATCCTC 57.558 50.000 0.00 0.00 0.00 3.71
53 54 5.759963 ACCTTAAGATTATAGAGCGTGACG 58.240 41.667 3.36 0.00 0.00 4.35
54 55 7.201145 TGAACCTTAAGATTATAGAGCGTGAC 58.799 38.462 3.36 0.00 0.00 3.67
55 56 7.342769 TGAACCTTAAGATTATAGAGCGTGA 57.657 36.000 3.36 0.00 0.00 4.35
56 57 8.420374 TTTGAACCTTAAGATTATAGAGCGTG 57.580 34.615 3.36 0.00 0.00 5.34
57 58 8.880750 GTTTTGAACCTTAAGATTATAGAGCGT 58.119 33.333 3.36 0.00 0.00 5.07
58 59 8.879759 TGTTTTGAACCTTAAGATTATAGAGCG 58.120 33.333 3.36 0.00 0.00 5.03
65 66 9.621629 TGAAGTCTGTTTTGAACCTTAAGATTA 57.378 29.630 3.36 0.00 0.00 1.75
66 67 8.406297 GTGAAGTCTGTTTTGAACCTTAAGATT 58.594 33.333 3.36 0.00 0.00 2.40
67 68 7.775561 AGTGAAGTCTGTTTTGAACCTTAAGAT 59.224 33.333 3.36 0.00 0.00 2.40
68 69 7.110155 AGTGAAGTCTGTTTTGAACCTTAAGA 58.890 34.615 3.36 0.00 0.00 2.10
69 70 7.321745 AGTGAAGTCTGTTTTGAACCTTAAG 57.678 36.000 0.00 0.00 0.00 1.85
70 71 6.036735 CGAGTGAAGTCTGTTTTGAACCTTAA 59.963 38.462 0.00 0.00 0.00 1.85
71 72 5.522460 CGAGTGAAGTCTGTTTTGAACCTTA 59.478 40.000 0.00 0.00 0.00 2.69
72 73 4.332819 CGAGTGAAGTCTGTTTTGAACCTT 59.667 41.667 0.00 0.00 0.00 3.50
73 74 3.871594 CGAGTGAAGTCTGTTTTGAACCT 59.128 43.478 0.00 0.00 0.00 3.50
74 75 3.621715 ACGAGTGAAGTCTGTTTTGAACC 59.378 43.478 0.00 0.00 0.00 3.62
75 76 4.548346 CGACGAGTGAAGTCTGTTTTGAAC 60.548 45.833 0.00 0.00 36.53 3.18
76 77 3.550275 CGACGAGTGAAGTCTGTTTTGAA 59.450 43.478 0.00 0.00 36.53 2.69
77 78 3.113322 CGACGAGTGAAGTCTGTTTTGA 58.887 45.455 0.00 0.00 36.53 2.69
78 79 3.113322 TCGACGAGTGAAGTCTGTTTTG 58.887 45.455 0.00 0.00 36.53 2.44
79 80 3.431922 TCGACGAGTGAAGTCTGTTTT 57.568 42.857 0.00 0.00 36.53 2.43
80 81 3.431922 TTCGACGAGTGAAGTCTGTTT 57.568 42.857 0.00 0.00 36.53 2.83
81 82 3.114065 GTTTCGACGAGTGAAGTCTGTT 58.886 45.455 0.00 0.00 36.53 3.16
82 83 2.543238 GGTTTCGACGAGTGAAGTCTGT 60.543 50.000 0.00 0.00 36.53 3.41
83 84 2.052157 GGTTTCGACGAGTGAAGTCTG 58.948 52.381 0.00 0.00 36.53 3.51
84 85 1.000496 GGGTTTCGACGAGTGAAGTCT 60.000 52.381 0.00 0.00 36.53 3.24
85 86 1.416373 GGGTTTCGACGAGTGAAGTC 58.584 55.000 0.00 0.00 35.41 3.01
86 87 0.033090 GGGGTTTCGACGAGTGAAGT 59.967 55.000 0.00 0.00 0.00 3.01
87 88 0.317479 AGGGGTTTCGACGAGTGAAG 59.683 55.000 0.00 0.00 0.00 3.02
88 89 0.754472 AAGGGGTTTCGACGAGTGAA 59.246 50.000 0.00 0.00 0.00 3.18
89 90 0.754472 AAAGGGGTTTCGACGAGTGA 59.246 50.000 0.00 0.00 0.00 3.41
90 91 0.865769 CAAAGGGGTTTCGACGAGTG 59.134 55.000 0.00 0.00 0.00 3.51
91 92 0.883370 GCAAAGGGGTTTCGACGAGT 60.883 55.000 0.00 0.00 0.00 4.18
92 93 1.574702 GGCAAAGGGGTTTCGACGAG 61.575 60.000 0.00 0.00 0.00 4.18
93 94 1.598685 GGCAAAGGGGTTTCGACGA 60.599 57.895 0.00 0.00 0.00 4.20
94 95 1.894756 TGGCAAAGGGGTTTCGACG 60.895 57.895 0.00 0.00 0.00 5.12
95 96 1.104577 TGTGGCAAAGGGGTTTCGAC 61.105 55.000 0.00 0.00 0.00 4.20
96 97 0.395862 TTGTGGCAAAGGGGTTTCGA 60.396 50.000 0.00 0.00 0.00 3.71
97 98 0.031994 CTTGTGGCAAAGGGGTTTCG 59.968 55.000 0.00 0.00 0.00 3.46
98 99 1.119684 ACTTGTGGCAAAGGGGTTTC 58.880 50.000 12.03 0.00 0.00 2.78
99 100 1.578897 AACTTGTGGCAAAGGGGTTT 58.421 45.000 12.03 0.00 0.00 3.27
100 101 1.578897 AAACTTGTGGCAAAGGGGTT 58.421 45.000 12.03 2.01 0.00 4.11
101 102 2.463047 TAAACTTGTGGCAAAGGGGT 57.537 45.000 12.03 0.00 0.00 4.95
102 103 4.350368 AAATAAACTTGTGGCAAAGGGG 57.650 40.909 12.03 0.00 0.00 4.79
103 104 6.756542 GCTATAAATAAACTTGTGGCAAAGGG 59.243 38.462 12.03 0.00 0.00 3.95
104 105 6.756542 GGCTATAAATAAACTTGTGGCAAAGG 59.243 38.462 12.03 0.18 0.00 3.11
105 106 7.319646 TGGCTATAAATAAACTTGTGGCAAAG 58.680 34.615 0.00 0.00 0.00 2.77
106 107 7.233389 TGGCTATAAATAAACTTGTGGCAAA 57.767 32.000 0.00 0.00 0.00 3.68
107 108 6.842437 TGGCTATAAATAAACTTGTGGCAA 57.158 33.333 0.00 0.00 0.00 4.52
108 109 6.842437 TTGGCTATAAATAAACTTGTGGCA 57.158 33.333 0.00 0.00 0.00 4.92
109 110 8.541133 TTTTTGGCTATAAATAAACTTGTGGC 57.459 30.769 0.00 0.00 0.00 5.01
131 132 6.875195 TCTCGGAAATTATACGGTCAGTTTTT 59.125 34.615 0.00 0.00 0.00 1.94
132 133 6.400568 TCTCGGAAATTATACGGTCAGTTTT 58.599 36.000 0.00 0.00 0.00 2.43
133 134 5.969423 TCTCGGAAATTATACGGTCAGTTT 58.031 37.500 0.00 0.00 0.00 2.66
134 135 5.587388 TCTCGGAAATTATACGGTCAGTT 57.413 39.130 0.00 0.00 0.00 3.16
135 136 5.587388 TTCTCGGAAATTATACGGTCAGT 57.413 39.130 0.00 0.00 0.00 3.41
136 137 6.897259 TTTTCTCGGAAATTATACGGTCAG 57.103 37.500 0.81 0.00 0.00 3.51
164 165 2.660064 GGCACTGGACGATGGGAGT 61.660 63.158 0.00 0.00 0.00 3.85
165 166 2.187946 GGCACTGGACGATGGGAG 59.812 66.667 0.00 0.00 0.00 4.30
230 246 3.487372 CGTCTCCAGAGATACCATACCA 58.513 50.000 0.00 0.00 39.97 3.25
231 247 2.229302 GCGTCTCCAGAGATACCATACC 59.771 54.545 0.00 0.00 39.97 2.73
232 248 2.095668 CGCGTCTCCAGAGATACCATAC 60.096 54.545 0.00 0.00 39.97 2.39
233 249 2.152016 CGCGTCTCCAGAGATACCATA 58.848 52.381 0.00 0.00 39.97 2.74
234 250 0.955178 CGCGTCTCCAGAGATACCAT 59.045 55.000 0.00 0.00 39.97 3.55
408 435 3.673323 CGCTGGAATAAAAAGGCACCTTC 60.673 47.826 1.61 0.00 34.84 3.46
431 458 2.554893 TCGAAACCCAAAATGTAGCACC 59.445 45.455 0.00 0.00 0.00 5.01
443 470 3.350612 CGCGCCTTTCGAAACCCA 61.351 61.111 6.47 0.00 41.67 4.51
444 471 4.097863 CCGCGCCTTTCGAAACCC 62.098 66.667 6.47 0.00 41.67 4.11
561 595 3.488553 GGTCAAATCCGGGCGAATAAAAG 60.489 47.826 0.00 0.00 0.00 2.27
624 658 0.738975 GCGCCCATTAAGAAACCTCC 59.261 55.000 0.00 0.00 0.00 4.30
626 660 1.029947 CCGCGCCCATTAAGAAACCT 61.030 55.000 0.00 0.00 0.00 3.50
689 730 2.046217 GTCGTTTCCCCCTGCCTC 60.046 66.667 0.00 0.00 0.00 4.70
693 734 2.742372 CGCTGTCGTTTCCCCCTG 60.742 66.667 0.00 0.00 0.00 4.45
694 735 4.016706 CCGCTGTCGTTTCCCCCT 62.017 66.667 0.00 0.00 0.00 4.79
732 773 1.266175 CGCATTTGATCCTGATCCTGC 59.734 52.381 4.76 9.56 37.02 4.85
924 970 2.941025 AGATGGTGGGGTGGGGTG 60.941 66.667 0.00 0.00 0.00 4.61
998 1044 2.764128 GCCCCTCCGACTCCATCA 60.764 66.667 0.00 0.00 0.00 3.07
1432 1493 4.144727 GGAGGAGGCGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1776 1837 4.243008 TGTGGCGCGGACTGGAAA 62.243 61.111 8.83 0.00 0.00 3.13
2216 2283 7.393234 TCAAGAATAATTAGGGACAACCAACAG 59.607 37.037 0.00 0.00 43.89 3.16
2279 2346 6.159299 TGGAAATCATCAACAAAGCTCAAA 57.841 33.333 0.00 0.00 0.00 2.69
2383 2462 2.032681 AAGCTGGTGTTCGCCTCC 59.967 61.111 4.05 0.00 0.00 4.30
2384 2463 0.884704 TTCAAGCTGGTGTTCGCCTC 60.885 55.000 4.05 0.00 0.00 4.70
2387 2466 2.422276 ATTTTCAAGCTGGTGTTCGC 57.578 45.000 0.00 0.00 0.00 4.70
2391 2470 6.096846 AGTTAACAGAATTTTCAAGCTGGTGT 59.903 34.615 8.61 0.00 32.82 4.16
2392 2471 6.507023 AGTTAACAGAATTTTCAAGCTGGTG 58.493 36.000 8.61 0.00 32.82 4.17
2394 2473 6.974965 AGAGTTAACAGAATTTTCAAGCTGG 58.025 36.000 8.61 0.00 32.82 4.85
2489 2578 5.182760 AGCATGCCTTTTCTTCTCTGTAAAG 59.817 40.000 15.66 0.00 0.00 1.85
2552 2641 8.914654 CAAGCGATGTGAAAATCAAAAGAATTA 58.085 29.630 0.00 0.00 0.00 1.40
2577 2667 0.315886 CAGCAATCCAAGCAGCAACA 59.684 50.000 0.00 0.00 0.00 3.33
2618 2708 5.914898 AGGAAATTAATTCGGTCAAAGGG 57.085 39.130 0.10 0.00 39.05 3.95
2619 2709 8.220755 TGATAGGAAATTAATTCGGTCAAAGG 57.779 34.615 0.10 0.00 39.05 3.11
2623 2713 9.627123 AGAAATGATAGGAAATTAATTCGGTCA 57.373 29.630 0.10 3.27 39.05 4.02
2624 2714 9.884465 CAGAAATGATAGGAAATTAATTCGGTC 57.116 33.333 0.10 0.00 39.05 4.79
2625 2715 8.352942 GCAGAAATGATAGGAAATTAATTCGGT 58.647 33.333 0.10 0.00 39.05 4.69
2626 2716 8.571336 AGCAGAAATGATAGGAAATTAATTCGG 58.429 33.333 0.10 0.00 39.05 4.30
2627 2717 9.956720 AAGCAGAAATGATAGGAAATTAATTCG 57.043 29.630 0.10 0.00 39.05 3.34
2631 2721 9.466497 ACAGAAGCAGAAATGATAGGAAATTAA 57.534 29.630 0.00 0.00 0.00 1.40
2633 2723 7.951347 ACAGAAGCAGAAATGATAGGAAATT 57.049 32.000 0.00 0.00 0.00 1.82
2634 2724 9.466497 TTTACAGAAGCAGAAATGATAGGAAAT 57.534 29.630 0.00 0.00 0.00 2.17
2635 2725 8.862325 TTTACAGAAGCAGAAATGATAGGAAA 57.138 30.769 0.00 0.00 0.00 3.13
2780 2871 7.946207 TGTGCAGTAAATTCCTGTTTATTTGA 58.054 30.769 0.00 0.00 32.41 2.69
2788 2879 4.460382 CCTGATTGTGCAGTAAATTCCTGT 59.540 41.667 0.00 0.00 34.06 4.00
2850 2942 4.502016 ACTGTAGCAACATGATGAGACAG 58.498 43.478 24.02 24.02 39.01 3.51
2851 2943 4.498241 GACTGTAGCAACATGATGAGACA 58.502 43.478 7.22 8.40 34.37 3.41
2860 2952 4.357918 AAAGACAGGACTGTAGCAACAT 57.642 40.909 4.73 0.00 45.05 2.71
3000 3100 7.704789 AAATGAATTCAAAGACAAGCAAGTC 57.295 32.000 13.09 0.70 38.81 3.01


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

AutoCloner maintained by Alex Coulton.