Multiple sequence alignment - TraesCS2D01G561600

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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 TraesCS2D01G561600 chr2D 100.000 3167 0 0 1 3167 633837358 633834192 0.000000e+00 5849.0
1 TraesCS2D01G561600 chr2D 90.000 240 15 2 1188 1427 633836105 633835875 5.130000e-78 302.0
2 TraesCS2D01G561600 chr2D 90.000 240 15 2 1254 1484 633836171 633835932 5.130000e-78 302.0
3 TraesCS2D01G561600 chr2D 82.514 183 14 6 1320 1484 633836171 633835989 9.160000e-31 145.0
4 TraesCS2D01G561600 chr2A 88.809 3208 172 80 44 3132 779844739 779847878 0.000000e+00 3762.0
5 TraesCS2D01G561600 chr2A 86.347 271 19 6 1251 1503 779845906 779846176 2.410000e-71 279.0
6 TraesCS2D01G561600 chr2A 84.921 252 29 2 1185 1427 779845972 779846223 2.440000e-61 246.0
7 TraesCS2D01G561600 chr2A 86.574 216 19 5 1830 2043 779849581 779849788 2.460000e-56 230.0
8 TraesCS2D01G561600 chr2A 86.022 186 26 0 1185 1370 779846038 779846223 1.930000e-47 200.0
9 TraesCS2D01G561600 chr2B 93.361 1446 56 11 824 2257 776806873 776805456 0.000000e+00 2102.0
10 TraesCS2D01G561600 chr2B 89.167 240 17 4 1254 1484 776806521 776806282 1.110000e-74 291.0
11 TraesCS2D01G561600 chr2B 89.744 234 13 4 1188 1420 776806455 776806232 4.000000e-74 289.0
12 TraesCS2D01G561600 chrUn 97.143 35 1 0 2684 2718 63521952 63521986 3.410000e-05 60.2
13 TraesCS2D01G561600 chrUn 97.143 35 1 0 2684 2718 321210685 321210719 3.410000e-05 60.2
14 TraesCS2D01G561600 chrUn 97.143 35 1 0 2684 2718 337835728 337835762 3.410000e-05 60.2
15 TraesCS2D01G561600 chrUn 97.143 35 1 0 2684 2718 388612143 388612109 3.410000e-05 60.2
16 TraesCS2D01G561600 chrUn 96.970 33 1 0 1 33 134274019 134274051 4.410000e-04 56.5
17 TraesCS2D01G561600 chr5A 97.143 35 1 0 2684 2718 555238930 555238896 3.410000e-05 60.2
18 TraesCS2D01G561600 chr5A 97.143 35 1 0 2684 2718 555253137 555253103 3.410000e-05 60.2
19 TraesCS2D01G561600 chr7A 96.970 33 1 0 1 33 85645937 85645969 4.410000e-04 56.5
20 TraesCS2D01G561600 chr7A 96.970 33 1 0 1 33 191175567 191175535 4.410000e-04 56.5
21 TraesCS2D01G561600 chr7A 96.970 33 1 0 1 33 210690303 210690271 4.410000e-04 56.5
22 TraesCS2D01G561600 chr6D 96.970 33 1 0 2749 2781 9820554 9820586 4.410000e-04 56.5
23 TraesCS2D01G561600 chr6D 96.970 33 1 0 1 33 37451205 37451237 4.410000e-04 56.5
24 TraesCS2D01G561600 chr6B 96.970 33 1 0 1 33 653216610 653216578 4.410000e-04 56.5
25 TraesCS2D01G561600 chr5D 96.970 33 1 0 1 33 449961050 449961082 4.410000e-04 56.5
26 TraesCS2D01G561600 chr5B 96.970 33 1 0 1 33 80202560 80202592 4.410000e-04 56.5
27 TraesCS2D01G561600 chr3B 86.538 52 5 1 2754 2805 764303074 764303123 4.410000e-04 56.5
28 TraesCS2D01G561600 chr1A 96.970 33 1 0 1 33 24301681 24301649 4.410000e-04 56.5
29 TraesCS2D01G561600 chr1A 94.286 35 2 0 2747 2781 486749495 486749529 2.000000e-03 54.7
30 TraesCS2D01G561600 chr7D 100.000 29 0 0 2691 2719 356897742 356897714 2.000000e-03 54.7


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 TraesCS2D01G561600 chr2D 633834192 633837358 3166 True 1649.5 5849 90.628500 1 3167 4 chr2D.!!$R1 3166
1 TraesCS2D01G561600 chr2A 779844739 779849788 5049 False 943.4 3762 86.534600 44 3132 5 chr2A.!!$F1 3088
2 TraesCS2D01G561600 chr2B 776805456 776806873 1417 True 894.0 2102 90.757333 824 2257 3 chr2B.!!$R1 1433

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
811 860 0.03563 CCTTCCTTCCTGAGGCTGTG 60.036 60.0 0.0 0.0 45.87 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 2696 0.03582 ACATGTTTGTACGGCCGGAT 60.036 50.0 31.76 12.49 33.16 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
22 23 3.477346 GGAACCCTAGGTCGCCCC 61.477 72.222 8.29 0.00 33.12 5.80
23 24 3.477346 GAACCCTAGGTCGCCCCC 61.477 72.222 8.29 0.00 33.12 5.40
27 28 4.835891 CCTAGGTCGCCCCCGAGT 62.836 72.222 0.00 0.00 45.38 4.18
28 29 3.217743 CTAGGTCGCCCCCGAGTC 61.218 72.222 0.00 0.00 45.38 3.36
29 30 3.717924 CTAGGTCGCCCCCGAGTCT 62.718 68.421 0.00 0.00 45.38 3.24
30 31 3.711059 TAGGTCGCCCCCGAGTCTC 62.711 68.421 0.00 0.00 45.38 3.36
35 36 3.090532 GCCCCCGAGTCTCCCAAT 61.091 66.667 0.00 0.00 0.00 3.16
36 37 3.108288 GCCCCCGAGTCTCCCAATC 62.108 68.421 0.00 0.00 0.00 2.67
37 38 1.383248 CCCCCGAGTCTCCCAATCT 60.383 63.158 0.00 0.00 0.00 2.40
38 39 0.105658 CCCCCGAGTCTCCCAATCTA 60.106 60.000 0.00 0.00 0.00 1.98
39 40 1.691482 CCCCCGAGTCTCCCAATCTAA 60.691 57.143 0.00 0.00 0.00 2.10
40 41 2.116238 CCCCGAGTCTCCCAATCTAAA 58.884 52.381 0.00 0.00 0.00 1.85
41 42 2.158943 CCCCGAGTCTCCCAATCTAAAC 60.159 54.545 0.00 0.00 0.00 2.01
42 43 2.500098 CCCGAGTCTCCCAATCTAAACA 59.500 50.000 0.00 0.00 0.00 2.83
43 44 3.134804 CCCGAGTCTCCCAATCTAAACAT 59.865 47.826 0.00 0.00 0.00 2.71
44 45 4.344102 CCCGAGTCTCCCAATCTAAACATA 59.656 45.833 0.00 0.00 0.00 2.29
45 46 5.012148 CCCGAGTCTCCCAATCTAAACATAT 59.988 44.000 0.00 0.00 0.00 1.78
46 47 6.210784 CCCGAGTCTCCCAATCTAAACATATA 59.789 42.308 0.00 0.00 0.00 0.86
47 48 7.316640 CCGAGTCTCCCAATCTAAACATATAG 58.683 42.308 0.00 0.00 0.00 1.31
48 49 7.316640 CGAGTCTCCCAATCTAAACATATAGG 58.683 42.308 0.00 0.00 0.00 2.57
49 50 7.039644 CGAGTCTCCCAATCTAAACATATAGGT 60.040 40.741 0.00 0.00 0.00 3.08
50 51 7.967908 AGTCTCCCAATCTAAACATATAGGTG 58.032 38.462 0.00 0.00 0.00 4.00
51 52 7.569111 AGTCTCCCAATCTAAACATATAGGTGT 59.431 37.037 0.00 0.00 0.00 4.16
52 53 8.867097 GTCTCCCAATCTAAACATATAGGTGTA 58.133 37.037 0.00 0.00 0.00 2.90
53 54 9.090103 TCTCCCAATCTAAACATATAGGTGTAG 57.910 37.037 8.21 8.21 31.10 2.74
154 158 4.431131 AATGCTCTGGTGGGCCGG 62.431 66.667 0.00 0.00 42.59 6.13
193 200 5.392380 GGCGCATGCAGCTAATAATATCTTT 60.392 40.000 25.77 0.00 45.35 2.52
199 206 9.608617 CATGCAGCTAATAATATCTTTTGTCTG 57.391 33.333 0.00 0.00 0.00 3.51
201 208 9.049523 TGCAGCTAATAATATCTTTTGTCTGAG 57.950 33.333 0.00 0.00 0.00 3.35
232 239 8.611757 AGTTAATCATTTTTCAGGTTTTGCAAC 58.388 29.630 0.00 0.00 0.00 4.17
240 247 3.565307 TCAGGTTTTGCAACATTCCTCT 58.435 40.909 0.00 0.00 34.15 3.69
252 259 7.327214 TGCAACATTCCTCTTTTAAGTTTGTT 58.673 30.769 0.00 0.00 0.00 2.83
277 284 7.881775 TTATCAATTTTAGGAAGGAGAAGGC 57.118 36.000 0.00 0.00 0.00 4.35
296 303 4.998051 AGGCTCCTTCTGGTTTTATTTCA 58.002 39.130 0.00 0.00 34.23 2.69
297 304 5.583932 AGGCTCCTTCTGGTTTTATTTCAT 58.416 37.500 0.00 0.00 34.23 2.57
298 305 6.019108 AGGCTCCTTCTGGTTTTATTTCATT 58.981 36.000 0.00 0.00 34.23 2.57
299 306 6.498303 AGGCTCCTTCTGGTTTTATTTCATTT 59.502 34.615 0.00 0.00 34.23 2.32
300 307 7.016563 AGGCTCCTTCTGGTTTTATTTCATTTT 59.983 33.333 0.00 0.00 34.23 1.82
301 308 7.661437 GGCTCCTTCTGGTTTTATTTCATTTTT 59.339 33.333 0.00 0.00 34.23 1.94
330 337 4.584327 TTTCTTTACTCAGCTTTTGGGC 57.416 40.909 0.00 0.00 0.00 5.36
331 338 3.508845 TCTTTACTCAGCTTTTGGGCT 57.491 42.857 0.00 0.00 44.10 5.19
332 339 3.832527 TCTTTACTCAGCTTTTGGGCTT 58.167 40.909 0.00 0.00 41.00 4.35
333 340 3.821033 TCTTTACTCAGCTTTTGGGCTTC 59.179 43.478 0.00 0.00 41.00 3.86
335 342 4.634012 TTACTCAGCTTTTGGGCTTCTA 57.366 40.909 0.00 0.00 41.00 2.10
502 518 4.599047 TGAAAAATGTTCGCCCTGAAAT 57.401 36.364 0.00 0.00 38.60 2.17
503 519 5.713792 TGAAAAATGTTCGCCCTGAAATA 57.286 34.783 0.00 0.00 38.60 1.40
506 522 5.659440 AAAATGTTCGCCCTGAAATATGT 57.341 34.783 0.00 0.00 38.60 2.29
515 531 9.048446 GTTCGCCCTGAAATATGTTAGTAATTA 57.952 33.333 0.00 0.00 38.60 1.40
601 637 9.987272 AAAATGTTCCCAAATTTTTGAAAAACA 57.013 22.222 5.08 10.82 40.55 2.83
643 679 8.726870 TTCTATAGAAAACCATAGGAAAACCG 57.273 34.615 12.87 0.00 0.00 4.44
675 711 9.599866 ACTAAAGGAAAACAGGAAAAATGAAAG 57.400 29.630 0.00 0.00 0.00 2.62
676 712 7.864108 AAAGGAAAACAGGAAAAATGAAAGG 57.136 32.000 0.00 0.00 0.00 3.11
715 764 0.527817 CGCCCGTCTCGCTCTTTTAT 60.528 55.000 0.00 0.00 0.00 1.40
720 769 2.159226 CCGTCTCGCTCTTTTATGGACT 60.159 50.000 0.00 0.00 0.00 3.85
722 771 3.304559 CGTCTCGCTCTTTTATGGACTTG 59.695 47.826 0.00 0.00 0.00 3.16
732 781 7.308830 GCTCTTTTATGGACTTGTTGTTCATCT 60.309 37.037 0.00 0.00 40.79 2.90
794 843 0.976641 TGACGGACTCATGCTTTCCT 59.023 50.000 5.77 0.00 0.00 3.36
810 859 0.178891 TCCTTCCTTCCTGAGGCTGT 60.179 55.000 0.00 0.00 45.87 4.40
811 860 0.035630 CCTTCCTTCCTGAGGCTGTG 60.036 60.000 0.00 0.00 45.87 3.66
858 907 3.965258 ATGCCTGACCGTGCCCAA 61.965 61.111 0.00 0.00 0.00 4.12
987 1036 1.150081 CACCCTCCTCATCCATGGC 59.850 63.158 6.96 0.00 0.00 4.40
988 1037 1.005289 ACCCTCCTCATCCATGGCT 59.995 57.895 6.96 0.00 0.00 4.75
1013 1062 2.048498 CGCAGCGCTATAAATACGACA 58.952 47.619 10.99 0.00 0.00 4.35
1014 1063 2.469886 CGCAGCGCTATAAATACGACAA 59.530 45.455 10.99 0.00 0.00 3.18
1069 1121 1.300620 GAGTGGTAGCACACGCACA 60.301 57.895 25.75 0.00 45.80 4.57
1613 1687 1.452108 GTTGGAGGGGATGAAGCCG 60.452 63.158 0.00 0.00 0.00 5.52
2003 2116 1.227342 TGCATGTGTGGTGTAGCGTG 61.227 55.000 0.00 0.00 0.00 5.34
2155 2274 6.015180 CCTTTCTGGTGAGAAATTTGGATGAA 60.015 38.462 0.00 0.00 45.25 2.57
2156 2275 6.975196 TTCTGGTGAGAAATTTGGATGAAA 57.025 33.333 0.00 0.00 35.14 2.69
2157 2276 7.543359 TTCTGGTGAGAAATTTGGATGAAAT 57.457 32.000 0.00 0.00 35.14 2.17
2158 2277 7.543359 TCTGGTGAGAAATTTGGATGAAATT 57.457 32.000 0.00 0.00 44.66 1.82
2159 2278 8.648698 TCTGGTGAGAAATTTGGATGAAATTA 57.351 30.769 0.00 0.00 42.41 1.40
2219 2338 8.579682 AACTTGTTTGCTCAATTATCAGAAAC 57.420 30.769 0.00 0.00 0.00 2.78
2386 2505 9.771534 AATAAGCTAATTGAGAGATGTTCTACC 57.228 33.333 0.00 0.00 35.87 3.18
2492 2611 6.263516 ACATTCACCAATCAAGAGTCAATG 57.736 37.500 0.00 0.00 0.00 2.82
2495 2614 4.717877 TCACCAATCAAGAGTCAATGTGT 58.282 39.130 0.00 0.00 0.00 3.72
2496 2615 4.756642 TCACCAATCAAGAGTCAATGTGTC 59.243 41.667 0.00 0.00 0.00 3.67
2497 2616 3.748048 ACCAATCAAGAGTCAATGTGTCG 59.252 43.478 0.00 0.00 0.00 4.35
2498 2617 3.996363 CCAATCAAGAGTCAATGTGTCGA 59.004 43.478 0.00 0.00 0.00 4.20
2499 2618 4.452114 CCAATCAAGAGTCAATGTGTCGAA 59.548 41.667 0.00 0.00 0.00 3.71
2500 2619 5.049474 CCAATCAAGAGTCAATGTGTCGAAA 60.049 40.000 0.00 0.00 0.00 3.46
2501 2620 5.597813 ATCAAGAGTCAATGTGTCGAAAC 57.402 39.130 0.00 0.00 0.00 2.78
2513 2632 3.550275 TGTGTCGAAACTCAAAACTCTCG 59.450 43.478 7.37 0.00 0.00 4.04
2519 2638 3.764237 AACTCAAAACTCTCGGCCTTA 57.236 42.857 0.00 0.00 0.00 2.69
2536 2655 5.221461 CGGCCTTAGTACATGGAGAATAGTT 60.221 44.000 0.00 0.00 0.00 2.24
2537 2656 6.224584 GGCCTTAGTACATGGAGAATAGTTC 58.775 44.000 0.00 0.00 0.00 3.01
2562 2681 2.787473 TTTGCGAGGACATGGAGAAT 57.213 45.000 0.00 0.00 0.00 2.40
2576 2695 4.350368 TGGAGAATAGTTCTTGTGTGCA 57.650 40.909 0.00 0.00 40.87 4.57
2577 2696 4.713553 TGGAGAATAGTTCTTGTGTGCAA 58.286 39.130 0.00 0.00 40.87 4.08
2584 2703 1.523154 TTCTTGTGTGCAATCCGGCC 61.523 55.000 0.00 0.00 33.65 6.13
2585 2704 3.326889 CTTGTGTGCAATCCGGCCG 62.327 63.158 21.04 21.04 33.65 6.13
2586 2705 4.634703 TGTGTGCAATCCGGCCGT 62.635 61.111 26.12 2.55 0.00 5.68
2587 2706 2.435234 GTGTGCAATCCGGCCGTA 60.435 61.111 26.12 9.32 0.00 4.02
2588 2707 2.435234 TGTGCAATCCGGCCGTAC 60.435 61.111 26.12 12.90 0.00 3.67
2589 2708 2.435234 GTGCAATCCGGCCGTACA 60.435 61.111 26.12 11.49 0.00 2.90
2590 2709 2.036006 GTGCAATCCGGCCGTACAA 61.036 57.895 26.12 6.83 0.00 2.41
2591 2710 1.302591 TGCAATCCGGCCGTACAAA 60.303 52.632 26.12 4.00 0.00 2.83
2592 2711 1.135939 GCAATCCGGCCGTACAAAC 59.864 57.895 26.12 4.87 0.00 2.93
2593 2712 1.579084 GCAATCCGGCCGTACAAACA 61.579 55.000 26.12 0.00 0.00 2.83
2610 2729 1.569708 ACATGTTTTTGCGTGCTTGG 58.430 45.000 0.00 0.00 0.00 3.61
2647 2766 0.038744 TTAACGACTCCCTCCGTCCT 59.961 55.000 0.00 0.00 38.13 3.85
2744 2871 1.587054 CGGCGTTTTTAATGGGGCA 59.413 52.632 0.00 0.00 0.00 5.36
2745 2872 0.174617 CGGCGTTTTTAATGGGGCAT 59.825 50.000 0.00 0.00 0.00 4.40
2796 2929 1.396996 CGAAACAATCCAGCCCTAACG 59.603 52.381 0.00 0.00 0.00 3.18
2800 2933 1.340991 ACAATCCAGCCCTAACGCATT 60.341 47.619 0.00 0.00 0.00 3.56
2833 2966 4.091424 GGATTTTTCGCACGAATCTTGAG 58.909 43.478 6.28 0.00 33.79 3.02
2890 3023 2.796500 GTTGAAACCAACCCGACCA 58.204 52.632 0.00 0.00 38.32 4.02
2911 3044 1.566211 ATGCTGCCACTACTCTGTCT 58.434 50.000 0.00 0.00 0.00 3.41
2912 3045 1.342074 TGCTGCCACTACTCTGTCTT 58.658 50.000 0.00 0.00 0.00 3.01
2926 3059 4.528987 ACTCTGTCTTACCTTCTTTCTCCC 59.471 45.833 0.00 0.00 0.00 4.30
2931 3064 2.735259 TACCTTCTTTCTCCCCCACT 57.265 50.000 0.00 0.00 0.00 4.00
2939 3072 3.330720 CTCCCCCACTCACCCACC 61.331 72.222 0.00 0.00 0.00 4.61
2940 3073 4.995058 TCCCCCACTCACCCACCC 62.995 72.222 0.00 0.00 0.00 4.61
2965 3098 1.616374 CGCCTCCTCTTATCCTCCTTC 59.384 57.143 0.00 0.00 0.00 3.46
2982 3115 0.758734 TTCTCACTCACCACCACCAG 59.241 55.000 0.00 0.00 0.00 4.00
2983 3116 1.302033 CTCACTCACCACCACCAGC 60.302 63.158 0.00 0.00 0.00 4.85
2993 3126 3.357079 CCACCAGCAGCCGTTGAC 61.357 66.667 0.00 0.00 0.00 3.18
3164 3308 1.970917 GATGCCACGAGCTTCCAACG 61.971 60.000 0.00 0.00 44.23 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.783288 CGACCTAGGGTTCCCTCGC 61.783 68.421 14.81 2.00 35.25 5.03
1 2 2.783288 GCGACCTAGGGTTCCCTCG 61.783 68.421 14.81 13.01 35.25 4.63
2 3 2.433146 GGCGACCTAGGGTTCCCTC 61.433 68.421 14.81 0.00 35.25 4.30
18 19 3.090532 ATTGGGAGACTCGGGGGC 61.091 66.667 0.00 0.00 0.00 5.80
19 20 0.105658 TAGATTGGGAGACTCGGGGG 60.106 60.000 0.00 0.00 0.00 5.40
20 21 1.789523 TTAGATTGGGAGACTCGGGG 58.210 55.000 0.00 0.00 0.00 5.73
21 22 2.500098 TGTTTAGATTGGGAGACTCGGG 59.500 50.000 0.00 0.00 0.00 5.14
22 23 3.887621 TGTTTAGATTGGGAGACTCGG 57.112 47.619 0.00 0.00 0.00 4.63
23 24 7.039644 ACCTATATGTTTAGATTGGGAGACTCG 60.040 40.741 0.00 0.00 0.00 4.18
24 25 8.091449 CACCTATATGTTTAGATTGGGAGACTC 58.909 40.741 0.00 0.00 0.00 3.36
25 26 7.569111 ACACCTATATGTTTAGATTGGGAGACT 59.431 37.037 0.00 0.00 0.00 3.24
26 27 7.736893 ACACCTATATGTTTAGATTGGGAGAC 58.263 38.462 0.00 0.00 0.00 3.36
27 28 7.931015 ACACCTATATGTTTAGATTGGGAGA 57.069 36.000 0.00 0.00 0.00 3.71
28 29 9.090103 TCTACACCTATATGTTTAGATTGGGAG 57.910 37.037 1.26 0.00 33.85 4.30
29 30 9.442062 TTCTACACCTATATGTTTAGATTGGGA 57.558 33.333 5.27 0.00 30.08 4.37
44 45 9.745880 CAACGTAGATGTTAATTCTACACCTAT 57.254 33.333 19.99 6.27 43.73 2.57
45 46 8.192774 CCAACGTAGATGTTAATTCTACACCTA 58.807 37.037 19.99 0.00 43.73 3.08
46 47 7.039882 CCAACGTAGATGTTAATTCTACACCT 58.960 38.462 19.99 0.00 43.73 4.00
47 48 7.037438 TCCAACGTAGATGTTAATTCTACACC 58.963 38.462 19.99 3.56 43.73 4.16
48 49 7.222224 CCTCCAACGTAGATGTTAATTCTACAC 59.778 40.741 19.99 5.74 43.73 2.90
49 50 7.262772 CCTCCAACGTAGATGTTAATTCTACA 58.737 38.462 19.99 0.14 43.73 2.74
50 51 6.200475 GCCTCCAACGTAGATGTTAATTCTAC 59.800 42.308 14.22 14.22 41.32 2.59
51 52 6.278363 GCCTCCAACGTAGATGTTAATTCTA 58.722 40.000 0.00 0.00 0.00 2.10
52 53 5.116882 GCCTCCAACGTAGATGTTAATTCT 58.883 41.667 0.00 0.00 0.00 2.40
53 54 4.025979 CGCCTCCAACGTAGATGTTAATTC 60.026 45.833 0.00 0.00 0.00 2.17
71 72 3.585862 TGTGTCAGATAAAACTCGCCTC 58.414 45.455 0.00 0.00 0.00 4.70
118 122 4.917415 GCATTCACTTTGCTTCGTTTATGT 59.083 37.500 0.00 0.00 37.14 2.29
172 176 8.295288 AGACAAAAGATATTATTAGCTGCATGC 58.705 33.333 11.82 11.82 43.29 4.06
173 177 9.608617 CAGACAAAAGATATTATTAGCTGCATG 57.391 33.333 1.02 0.00 0.00 4.06
175 179 8.962884 TCAGACAAAAGATATTATTAGCTGCA 57.037 30.769 1.02 0.00 0.00 4.41
176 180 9.265901 TCTCAGACAAAAGATATTATTAGCTGC 57.734 33.333 0.00 0.00 0.00 5.25
205 212 8.729805 TGCAAAACCTGAAAAATGATTAACTT 57.270 26.923 0.00 0.00 0.00 2.66
206 213 8.611757 GTTGCAAAACCTGAAAAATGATTAACT 58.388 29.630 0.00 0.00 0.00 2.24
207 214 8.394121 TGTTGCAAAACCTGAAAAATGATTAAC 58.606 29.630 0.00 0.00 0.00 2.01
208 215 8.498054 TGTTGCAAAACCTGAAAAATGATTAA 57.502 26.923 0.00 0.00 0.00 1.40
209 216 8.674263 ATGTTGCAAAACCTGAAAAATGATTA 57.326 26.923 0.00 0.00 0.00 1.75
210 217 6.998968 TGTTGCAAAACCTGAAAAATGATT 57.001 29.167 0.00 0.00 0.00 2.57
211 218 7.255208 GGAATGTTGCAAAACCTGAAAAATGAT 60.255 33.333 0.00 0.00 0.00 2.45
212 219 6.038050 GGAATGTTGCAAAACCTGAAAAATGA 59.962 34.615 0.00 0.00 0.00 2.57
213 220 6.038492 AGGAATGTTGCAAAACCTGAAAAATG 59.962 34.615 0.00 0.00 0.00 2.32
214 221 6.121590 AGGAATGTTGCAAAACCTGAAAAAT 58.878 32.000 0.00 0.00 0.00 1.82
215 222 5.495640 AGGAATGTTGCAAAACCTGAAAAA 58.504 33.333 0.00 0.00 0.00 1.94
216 223 5.096443 AGGAATGTTGCAAAACCTGAAAA 57.904 34.783 0.00 0.00 0.00 2.29
217 224 4.405358 AGAGGAATGTTGCAAAACCTGAAA 59.595 37.500 16.04 0.00 0.00 2.69
252 259 8.116026 AGCCTTCTCCTTCCTAAAATTGATAAA 58.884 33.333 0.00 0.00 0.00 1.40
478 494 4.599047 TCAGGGCGAACATTTTTCAAAT 57.401 36.364 0.00 0.00 0.00 2.32
482 498 6.099341 ACATATTTCAGGGCGAACATTTTTC 58.901 36.000 0.00 0.00 31.73 2.29
618 654 8.542080 TCGGTTTTCCTATGGTTTTCTATAGAA 58.458 33.333 11.24 11.24 41.81 2.10
619 655 8.081517 TCGGTTTTCCTATGGTTTTCTATAGA 57.918 34.615 0.00 0.00 41.81 1.98
620 656 8.726870 TTCGGTTTTCCTATGGTTTTCTATAG 57.273 34.615 0.00 0.00 39.88 1.31
649 685 9.599866 CTTTCATTTTTCCTGTTTTCCTTTAGT 57.400 29.630 0.00 0.00 0.00 2.24
651 687 7.990314 CCCTTTCATTTTTCCTGTTTTCCTTTA 59.010 33.333 0.00 0.00 0.00 1.85
670 706 2.282674 CTGCTGCTGGCCCTTTCA 60.283 61.111 0.00 0.00 40.92 2.69
692 728 1.870055 AAGAGCGAGACGGGCGTTTA 61.870 55.000 0.00 0.00 35.00 2.01
706 755 6.072112 TGAACAACAAGTCCATAAAAGAGC 57.928 37.500 0.00 0.00 0.00 4.09
715 764 4.780815 AGACAAGATGAACAACAAGTCCA 58.219 39.130 0.00 0.00 0.00 4.02
720 769 3.953612 AGGCAAGACAAGATGAACAACAA 59.046 39.130 0.00 0.00 0.00 2.83
722 771 4.154918 CCTAGGCAAGACAAGATGAACAAC 59.845 45.833 0.00 0.00 0.00 3.32
732 781 1.271840 ATCGGGCCTAGGCAAGACAA 61.272 55.000 34.09 13.73 44.11 3.18
811 860 2.357327 TGAATCAACTTGCTGCATGC 57.643 45.000 11.82 11.82 43.25 4.06
858 907 1.213013 GTCGTCGTGAGTGGATGCT 59.787 57.895 0.00 0.00 0.00 3.79
967 1016 1.150081 CATGGATGAGGAGGGTGCC 59.850 63.158 0.00 0.00 0.00 5.01
1013 1062 0.949397 TGTGTGAGCTACGAGACGTT 59.051 50.000 1.53 0.00 41.54 3.99
1014 1063 0.517755 CTGTGTGAGCTACGAGACGT 59.482 55.000 0.00 0.00 44.35 4.34
1069 1121 0.599204 CGCTGGAACTGTTGGTACGT 60.599 55.000 0.00 0.00 0.00 3.57
1071 1123 1.145803 GTCGCTGGAACTGTTGGTAC 58.854 55.000 0.00 0.00 0.00 3.34
1072 1124 0.034337 GGTCGCTGGAACTGTTGGTA 59.966 55.000 0.00 0.00 0.00 3.25
1445 1519 1.443407 CTCCTCCGATGGCGTGATT 59.557 57.895 0.00 0.00 35.23 2.57
2114 2233 8.356657 CACCAGAAAGGACATATAACAAAACAA 58.643 33.333 0.00 0.00 41.22 2.83
2158 2277 9.660180 GCATGGGGTAATTTTTATTCAAGTTTA 57.340 29.630 0.00 0.00 0.00 2.01
2159 2278 8.160106 TGCATGGGGTAATTTTTATTCAAGTTT 58.840 29.630 0.00 0.00 0.00 2.66
2219 2338 3.030291 AGACTGAAGGCTACTCATCCTG 58.970 50.000 0.00 0.00 32.00 3.86
2386 2505 1.529226 AGGTCAGTCGTCTCACTCTG 58.471 55.000 0.00 0.00 0.00 3.35
2492 2611 3.060473 CCGAGAGTTTTGAGTTTCGACAC 60.060 47.826 0.00 0.00 0.00 3.67
2495 2614 2.132762 GCCGAGAGTTTTGAGTTTCGA 58.867 47.619 0.00 0.00 0.00 3.71
2496 2615 1.194772 GGCCGAGAGTTTTGAGTTTCG 59.805 52.381 0.00 0.00 0.00 3.46
2497 2616 2.495084 AGGCCGAGAGTTTTGAGTTTC 58.505 47.619 0.00 0.00 0.00 2.78
2498 2617 2.640316 AGGCCGAGAGTTTTGAGTTT 57.360 45.000 0.00 0.00 0.00 2.66
2499 2618 2.640316 AAGGCCGAGAGTTTTGAGTT 57.360 45.000 0.00 0.00 0.00 3.01
2500 2619 2.633481 ACTAAGGCCGAGAGTTTTGAGT 59.367 45.455 14.03 0.00 0.00 3.41
2501 2620 3.320673 ACTAAGGCCGAGAGTTTTGAG 57.679 47.619 14.03 0.00 0.00 3.02
2513 2632 5.810080 ACTATTCTCCATGTACTAAGGCC 57.190 43.478 0.00 0.00 0.00 5.19
2562 2681 2.422597 CCGGATTGCACACAAGAACTA 58.577 47.619 0.00 0.00 39.69 2.24
2576 2695 1.091537 CATGTTTGTACGGCCGGATT 58.908 50.000 31.76 11.61 0.00 3.01
2577 2696 0.035820 ACATGTTTGTACGGCCGGAT 60.036 50.000 31.76 12.49 33.16 4.18
2584 2703 3.598225 GCACGCAAAAACATGTTTGTACG 60.598 43.478 25.69 25.69 40.06 3.67
2585 2704 3.549873 AGCACGCAAAAACATGTTTGTAC 59.450 39.130 23.93 12.75 40.06 2.90
2586 2705 3.775202 AGCACGCAAAAACATGTTTGTA 58.225 36.364 23.93 0.00 40.06 2.41
2587 2706 2.615869 AGCACGCAAAAACATGTTTGT 58.384 38.095 23.93 16.44 40.06 2.83
2588 2707 3.343990 CAAGCACGCAAAAACATGTTTG 58.656 40.909 23.93 14.55 40.72 2.93
2589 2708 2.351111 CCAAGCACGCAAAAACATGTTT 59.649 40.909 18.13 18.13 0.00 2.83
2590 2709 1.932511 CCAAGCACGCAAAAACATGTT 59.067 42.857 4.92 4.92 0.00 2.71
2591 2710 1.134848 ACCAAGCACGCAAAAACATGT 60.135 42.857 0.00 0.00 0.00 3.21
2592 2711 1.522258 GACCAAGCACGCAAAAACATG 59.478 47.619 0.00 0.00 0.00 3.21
2593 2712 1.537990 GGACCAAGCACGCAAAAACAT 60.538 47.619 0.00 0.00 0.00 2.71
2610 2729 5.180492 TCGTTAAGAAAACATGTCCATGGAC 59.820 40.000 33.97 33.97 42.91 4.02
2689 2808 3.641906 CCTCCGACCCATAATGTAAGACT 59.358 47.826 0.00 0.00 0.00 3.24
2776 2909 1.396996 CGTTAGGGCTGGATTGTTTCG 59.603 52.381 0.00 0.00 0.00 3.46
2800 2933 6.863645 TCGTGCGAAAAATCCAATGATAAAAA 59.136 30.769 0.00 0.00 0.00 1.94
2819 2952 1.291184 TGTGCCTCAAGATTCGTGCG 61.291 55.000 0.00 0.00 0.00 5.34
2833 2966 1.160137 GACATGGTGACTTCTGTGCC 58.840 55.000 0.00 0.00 0.00 5.01
2884 3017 0.676466 TAGTGGCAGCATTTGGTCGG 60.676 55.000 0.00 0.00 0.00 4.79
2889 3022 2.417933 GACAGAGTAGTGGCAGCATTTG 59.582 50.000 0.00 0.00 0.00 2.32
2890 3023 2.304180 AGACAGAGTAGTGGCAGCATTT 59.696 45.455 0.00 0.00 0.00 2.32
2911 3044 2.910977 GAGTGGGGGAGAAAGAAGGTAA 59.089 50.000 0.00 0.00 0.00 2.85
2912 3045 2.158066 TGAGTGGGGGAGAAAGAAGGTA 60.158 50.000 0.00 0.00 0.00 3.08
2939 3072 1.807495 GATAAGAGGAGGCGGTCGGG 61.807 65.000 0.00 0.00 0.00 5.14
2940 3073 1.660917 GATAAGAGGAGGCGGTCGG 59.339 63.158 0.00 0.00 0.00 4.79
2965 3098 1.302033 GCTGGTGGTGGTGAGTGAG 60.302 63.158 0.00 0.00 0.00 3.51
3010 3143 4.435970 TCCTCGCCGCACTCCCTA 62.436 66.667 0.00 0.00 0.00 3.53
3108 3241 2.597340 CATCCACCAATCCGGGCT 59.403 61.111 0.00 0.00 40.22 5.19
3109 3242 3.219198 GCATCCACCAATCCGGGC 61.219 66.667 0.00 0.00 40.22 6.13
3135 3279 2.581354 GTGGCATCGTGCTCCTCT 59.419 61.111 9.31 0.00 44.28 3.69
3141 3285 3.088500 GAAGCTCGTGGCATCGTGC 62.089 63.158 20.58 20.58 46.10 5.34


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

AutoCloner maintained by Alex Coulton.