Multiple sequence alignment - TraesCS3A01G264900

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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 TraesCS3A01G264900 chr3A 100.000 2470 0 0 1 2470 489312963 489310494 0.000000e+00 4562.0
1 TraesCS3A01G264900 chr3A 100.000 45 0 0 2426 2470 72476310 72476266 1.570000e-12 84.2
2 TraesCS3A01G264900 chr3D 90.564 2374 113 55 81 2414 367237868 367235566 0.000000e+00 3040.0
3 TraesCS3A01G264900 chr3B 90.501 2116 104 49 367 2430 478324052 478321982 0.000000e+00 2704.0
4 TraesCS3A01G264900 chr3B 85.393 356 29 11 1 354 478330643 478330309 5.060000e-92 348.0
5 TraesCS3A01G264900 chr1D 90.141 142 14 0 1001 1142 459880642 459880501 4.190000e-43 185.0
6 TraesCS3A01G264900 chr1D 92.553 94 7 0 1614 1707 459880277 459880184 4.280000e-28 135.0
7 TraesCS3A01G264900 chr1A 90.210 143 12 2 1001 1142 551593136 551592995 4.190000e-43 185.0
8 TraesCS3A01G264900 chr1A 91.837 98 7 1 1614 1711 551592780 551592684 4.280000e-28 135.0
9 TraesCS3A01G264900 chr1B 87.333 150 16 3 994 1142 631967724 631967577 4.220000e-38 169.0
10 TraesCS3A01G264900 chr1B 92.553 94 7 0 1614 1707 631967367 631967274 4.280000e-28 135.0
11 TraesCS3A01G264900 chr1B 100.000 43 0 0 2428 2470 10371693 10371651 2.040000e-11 80.5
12 TraesCS3A01G264900 chr5B 87.097 124 13 3 1004 1125 391144733 391144855 1.190000e-28 137.0
13 TraesCS3A01G264900 chr5B 82.482 137 14 9 1000 1131 585835966 585835835 7.220000e-21 111.0
14 TraesCS3A01G264900 chr5A 86.290 124 14 3 1004 1125 436089153 436089275 5.540000e-27 132.0
15 TraesCS3A01G264900 chr5A 100.000 45 0 0 2426 2470 633646318 633646274 1.570000e-12 84.2
16 TraesCS3A01G264900 chr7B 91.860 86 7 0 1609 1694 561280494 561280409 1.200000e-23 121.0
17 TraesCS3A01G264900 chr7B 97.872 47 1 0 2424 2470 72768475 72768429 5.660000e-12 82.4
18 TraesCS3A01G264900 chr7D 90.698 86 8 0 1609 1694 524915755 524915670 5.580000e-22 115.0
19 TraesCS3A01G264900 chr7A 90.698 86 8 0 1609 1694 604853602 604853517 5.580000e-22 115.0
20 TraesCS3A01G264900 chr7A 100.000 43 0 0 2428 2470 637300037 637299995 2.040000e-11 80.5
21 TraesCS3A01G264900 chr7A 100.000 43 0 0 2428 2470 637307113 637307071 2.040000e-11 80.5
22 TraesCS3A01G264900 chr6B 90.588 85 8 0 1610 1694 652629938 652629854 2.010000e-21 113.0
23 TraesCS3A01G264900 chr6B 95.918 49 2 0 2422 2470 514689117 514689165 2.040000e-11 80.5
24 TraesCS3A01G264900 chr5D 81.752 137 15 9 1000 1131 478222935 478222804 3.360000e-19 106.0
25 TraesCS3A01G264900 chrUn 100.000 43 0 0 2428 2470 303495319 303495277 2.040000e-11 80.5
26 TraesCS3A01G264900 chr2A 96.000 50 0 2 2422 2470 681192500 681192548 2.040000e-11 80.5


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 TraesCS3A01G264900 chr3A 489310494 489312963 2469 True 4562 4562 100.000 1 2470 1 chr3A.!!$R2 2469
1 TraesCS3A01G264900 chr3D 367235566 367237868 2302 True 3040 3040 90.564 81 2414 1 chr3D.!!$R1 2333
2 TraesCS3A01G264900 chr3B 478321982 478324052 2070 True 2704 2704 90.501 367 2430 1 chr3B.!!$R1 2063

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
338 340 0.101399 ACATTTGGCACGAAACGCAA 59.899 45.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2008 0.429736 CGCGTTGACGTTGTAGTGAG 59.57 55.0 0.0 0.0 42.22 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
24 25 7.364149 AGTAGATTTCAGAGATTGATCAGCT 57.636 36.000 0.00 0.00 35.27 4.24
25 26 7.794041 AGTAGATTTCAGAGATTGATCAGCTT 58.206 34.615 0.00 0.00 35.27 3.74
26 27 6.928979 AGATTTCAGAGATTGATCAGCTTG 57.071 37.500 0.00 0.74 35.27 4.01
27 28 5.823570 AGATTTCAGAGATTGATCAGCTTGG 59.176 40.000 0.00 0.00 35.27 3.61
28 29 2.915349 TCAGAGATTGATCAGCTTGGC 58.085 47.619 0.00 0.00 0.00 4.52
29 30 2.504585 TCAGAGATTGATCAGCTTGGCT 59.495 45.455 0.00 0.00 40.77 4.75
30 31 3.708121 TCAGAGATTGATCAGCTTGGCTA 59.292 43.478 0.00 0.00 36.40 3.93
31 32 4.347292 TCAGAGATTGATCAGCTTGGCTAT 59.653 41.667 0.00 0.00 36.40 2.97
32 33 5.541484 TCAGAGATTGATCAGCTTGGCTATA 59.459 40.000 0.00 0.00 36.40 1.31
33 34 5.638657 CAGAGATTGATCAGCTTGGCTATAC 59.361 44.000 0.00 0.00 36.40 1.47
34 35 5.543405 AGAGATTGATCAGCTTGGCTATACT 59.457 40.000 0.00 0.00 36.40 2.12
35 36 5.549347 AGATTGATCAGCTTGGCTATACTG 58.451 41.667 0.00 0.00 36.40 2.74
36 37 3.117491 TGATCAGCTTGGCTATACTGC 57.883 47.619 0.00 0.00 36.40 4.40
44 45 4.640855 GCTATACTGCCGCGGCGA 62.641 66.667 41.73 30.54 45.51 5.54
45 46 2.429236 CTATACTGCCGCGGCGAG 60.429 66.667 41.73 36.93 45.51 5.03
46 47 2.903350 TATACTGCCGCGGCGAGA 60.903 61.111 38.34 29.87 45.51 4.04
47 48 2.402282 CTATACTGCCGCGGCGAGAA 62.402 60.000 38.34 28.41 45.51 2.87
48 49 1.802337 TATACTGCCGCGGCGAGAAT 61.802 55.000 38.34 31.50 45.51 2.40
49 50 1.802337 ATACTGCCGCGGCGAGAATA 61.802 55.000 38.34 28.55 45.51 1.75
50 51 1.802337 TACTGCCGCGGCGAGAATAT 61.802 55.000 38.34 25.54 45.51 1.28
51 52 1.956170 CTGCCGCGGCGAGAATATT 60.956 57.895 41.73 0.00 45.51 1.28
52 53 2.162921 CTGCCGCGGCGAGAATATTG 62.163 60.000 41.73 19.69 45.51 1.90
53 54 2.954753 GCCGCGGCGAGAATATTGG 61.955 63.158 37.24 4.42 0.00 3.16
54 55 1.594293 CCGCGGCGAGAATATTGGT 60.594 57.895 25.92 0.00 0.00 3.67
55 56 1.564622 CGCGGCGAGAATATTGGTG 59.435 57.895 19.16 0.00 0.00 4.17
56 57 1.279840 GCGGCGAGAATATTGGTGC 59.720 57.895 12.98 0.00 0.00 5.01
57 58 1.436195 GCGGCGAGAATATTGGTGCA 61.436 55.000 12.98 0.00 0.00 4.57
58 59 0.583438 CGGCGAGAATATTGGTGCAG 59.417 55.000 0.00 0.00 0.00 4.41
59 60 1.668419 GGCGAGAATATTGGTGCAGT 58.332 50.000 0.00 0.00 0.00 4.40
60 61 2.017049 GGCGAGAATATTGGTGCAGTT 58.983 47.619 0.00 0.00 0.00 3.16
61 62 2.032178 GGCGAGAATATTGGTGCAGTTC 59.968 50.000 0.00 0.00 0.00 3.01
62 63 2.285834 GCGAGAATATTGGTGCAGTTCG 60.286 50.000 0.00 0.00 0.00 3.95
63 64 2.285220 CGAGAATATTGGTGCAGTTCGG 59.715 50.000 0.00 0.00 0.00 4.30
64 65 2.614057 GAGAATATTGGTGCAGTTCGGG 59.386 50.000 0.00 0.00 0.00 5.14
65 66 1.676006 GAATATTGGTGCAGTTCGGGG 59.324 52.381 0.00 0.00 0.00 5.73
66 67 0.623723 ATATTGGTGCAGTTCGGGGT 59.376 50.000 0.00 0.00 0.00 4.95
67 68 0.322098 TATTGGTGCAGTTCGGGGTG 60.322 55.000 0.00 0.00 0.00 4.61
68 69 4.947147 TGGTGCAGTTCGGGGTGC 62.947 66.667 0.00 0.00 40.29 5.01
97 98 2.266055 CTCACCTGCTCCCCGTTC 59.734 66.667 0.00 0.00 0.00 3.95
122 124 1.301716 TTTCAGCCCTGCGTCAGTC 60.302 57.895 6.19 0.00 0.00 3.51
139 141 4.021544 GTCAGTCTGACTCTGAAACTGGAT 60.022 45.833 23.25 0.00 43.73 3.41
140 142 4.219507 TCAGTCTGACTCTGAAACTGGATC 59.780 45.833 7.49 0.00 38.71 3.36
141 143 3.192422 AGTCTGACTCTGAAACTGGATCG 59.808 47.826 4.06 0.00 0.00 3.69
142 144 2.493675 TCTGACTCTGAAACTGGATCGG 59.506 50.000 0.00 0.00 0.00 4.18
173 175 1.667724 GGGTGCGACATTTCATCAGAG 59.332 52.381 0.00 0.00 0.00 3.35
191 193 1.095228 AGTTTCAGTGCCACCACACG 61.095 55.000 0.00 0.00 45.45 4.49
200 202 4.429212 CACCACACGCGGGATCGA 62.429 66.667 19.19 0.00 39.00 3.59
201 203 3.458163 ACCACACGCGGGATCGAT 61.458 61.111 19.19 0.00 39.00 3.59
202 204 2.658593 CCACACGCGGGATCGATC 60.659 66.667 19.19 17.36 39.00 3.69
204 206 4.266070 ACACGCGGGATCGATCGG 62.266 66.667 19.19 13.98 39.00 4.18
240 242 2.736995 CGCCAAGAAACGCGGAGA 60.737 61.111 12.47 0.00 44.57 3.71
241 243 2.314647 CGCCAAGAAACGCGGAGAA 61.315 57.895 12.47 0.00 44.57 2.87
263 265 3.217017 CTCAGGCGGCCGCTACTA 61.217 66.667 45.23 27.84 41.60 1.82
264 266 3.486252 CTCAGGCGGCCGCTACTAC 62.486 68.421 45.23 30.15 41.60 2.73
286 288 0.248661 ACGCGTCTTCCATCTGATCG 60.249 55.000 5.58 0.00 0.00 3.69
297 299 3.320256 TCCATCTGATCGATCCACTGAAG 59.680 47.826 22.31 11.82 0.00 3.02
299 301 2.034878 TCTGATCGATCCACTGAAGGG 58.965 52.381 22.31 2.42 0.00 3.95
301 303 2.432146 CTGATCGATCCACTGAAGGGAA 59.568 50.000 22.31 0.00 38.09 3.97
338 340 0.101399 ACATTTGGCACGAAACGCAA 59.899 45.000 0.00 0.00 0.00 4.85
441 457 0.109735 TCTCGCGCACAAGTACAGAG 60.110 55.000 8.75 2.17 0.00 3.35
461 480 6.381420 ACAGAGGGAGGAATTATATATGACCG 59.619 42.308 0.00 0.00 0.00 4.79
529 548 1.241990 ATGGCAGTCAACAGCAGCAG 61.242 55.000 0.00 0.00 0.00 4.24
686 713 2.436109 CACCTCCACCCACCCAAG 59.564 66.667 0.00 0.00 0.00 3.61
709 736 2.125552 TGATTGCTCAGACGCCCG 60.126 61.111 0.00 0.00 0.00 6.13
718 745 2.470821 CTCAGACGCCCGGTATAAAAG 58.529 52.381 0.00 0.00 0.00 2.27
719 746 1.137479 TCAGACGCCCGGTATAAAAGG 59.863 52.381 0.00 0.00 0.00 3.11
720 747 0.179065 AGACGCCCGGTATAAAAGGC 60.179 55.000 0.00 0.00 42.18 4.35
755 788 0.984230 TGCAAGCCTACTAGCCTTGT 59.016 50.000 8.25 0.00 0.00 3.16
779 820 3.617143 TTCCATCTGCTGCGCTGCT 62.617 57.895 34.26 16.27 0.00 4.24
780 821 3.877357 CCATCTGCTGCGCTGCTG 61.877 66.667 34.26 32.57 0.00 4.41
796 837 4.228567 TGCAACACCGCGAGTCCA 62.229 61.111 8.23 4.36 33.35 4.02
799 840 1.885388 CAACACCGCGAGTCCACAA 60.885 57.895 8.23 0.00 0.00 3.33
815 856 4.497984 AACGCACAGCACCACCCA 62.498 61.111 0.00 0.00 0.00 4.51
819 864 2.906897 CACAGCACCACCCACACC 60.907 66.667 0.00 0.00 0.00 4.16
820 865 4.562425 ACAGCACCACCCACACCG 62.562 66.667 0.00 0.00 0.00 4.94
856 905 1.538047 GCTGCAGGAAGGTTTGATCA 58.462 50.000 17.12 0.00 0.00 2.92
871 927 1.160137 GATCAATCCATACGCCCTGC 58.840 55.000 0.00 0.00 0.00 4.85
873 929 1.149174 CAATCCATACGCCCTGCCT 59.851 57.895 0.00 0.00 0.00 4.75
874 930 0.886490 CAATCCATACGCCCTGCCTC 60.886 60.000 0.00 0.00 0.00 4.70
903 959 4.434354 AGCGACGAGAGGCCTCCT 62.434 66.667 29.54 16.46 36.04 3.69
904 960 3.453679 GCGACGAGAGGCCTCCTT 61.454 66.667 29.54 12.24 36.04 3.36
905 961 2.802106 CGACGAGAGGCCTCCTTC 59.198 66.667 29.54 19.64 36.04 3.46
907 963 1.380650 GACGAGAGGCCTCCTTCCT 60.381 63.158 29.54 10.52 36.04 3.36
910 966 1.688884 GAGAGGCCTCCTTCCTGCT 60.689 63.158 29.54 7.98 31.76 4.24
912 968 3.080121 AGGCCTCCTTCCTGCTCG 61.080 66.667 0.00 0.00 31.53 5.03
913 969 4.847444 GGCCTCCTTCCTGCTCGC 62.847 72.222 0.00 0.00 0.00 5.03
935 991 3.680786 GGGCCGGCCTGTGTTTTC 61.681 66.667 42.70 21.56 36.10 2.29
948 1004 3.223435 TGTGTTTTCTTGGGCGGATTTA 58.777 40.909 0.00 0.00 0.00 1.40
991 1048 1.385756 GGTGGTAGAGCGAGAGGGAC 61.386 65.000 0.00 0.00 0.00 4.46
1142 1199 1.626654 CCGCAGAAAGCAGGTACGTG 61.627 60.000 11.20 11.20 46.13 4.49
1143 1200 1.497722 GCAGAAAGCAGGTACGTGC 59.502 57.895 28.56 28.56 44.79 5.34
1278 1335 2.549282 CGGCGTCGTCCTTTTGTG 59.451 61.111 0.00 0.00 0.00 3.33
1321 1400 2.762327 CCCATGGTTGCTAAGCTTTGAT 59.238 45.455 11.73 0.00 0.00 2.57
1490 1569 0.234106 CCGATTTAGCTGAGCGCATG 59.766 55.000 11.47 0.00 42.61 4.06
1508 1587 0.956902 TGTGCACTGAATCGCATGCT 60.957 50.000 19.41 0.00 40.89 3.79
1582 1661 3.917985 TGTCACGTAATTGACTGATCGTG 59.082 43.478 8.80 8.80 45.34 4.35
1583 1662 3.918591 GTCACGTAATTGACTGATCGTGT 59.081 43.478 13.49 0.00 45.33 4.49
1584 1663 4.030306 GTCACGTAATTGACTGATCGTGTC 59.970 45.833 13.49 10.58 45.33 3.67
1585 1664 4.082949 TCACGTAATTGACTGATCGTGTCT 60.083 41.667 16.24 3.36 45.33 3.41
1711 1793 3.845259 GCCATGGCCATGCACCAG 61.845 66.667 36.08 24.02 41.46 4.00
1724 1809 2.037136 CACCAGCAGCAGCAGTACC 61.037 63.158 3.17 0.00 45.49 3.34
1813 1898 2.326897 CAGAGCCAATGCGCATCG 59.673 61.111 25.53 13.45 44.33 3.84
2041 2126 0.957395 ACATGTTCTTGCCCGAGCTG 60.957 55.000 0.00 0.00 40.80 4.24
2275 2364 4.037923 ACAAAACCAAGCCACTAATGTCAG 59.962 41.667 0.00 0.00 0.00 3.51
2322 2415 1.825285 TAGTCGTCGATCGCCGTAGC 61.825 60.000 18.67 9.96 39.75 3.58
2430 2523 3.722147 CCACTCCACTGCTATGTCATAC 58.278 50.000 0.00 0.00 0.00 2.39
2431 2524 3.386078 CCACTCCACTGCTATGTCATACT 59.614 47.826 0.00 0.00 0.00 2.12
2432 2525 4.500545 CCACTCCACTGCTATGTCATACTC 60.501 50.000 0.00 0.00 0.00 2.59
2433 2526 3.639094 ACTCCACTGCTATGTCATACTCC 59.361 47.826 0.00 0.00 0.00 3.85
2434 2527 2.965831 TCCACTGCTATGTCATACTCCC 59.034 50.000 0.00 0.00 0.00 4.30
2435 2528 2.968574 CCACTGCTATGTCATACTCCCT 59.031 50.000 0.00 0.00 0.00 4.20
2436 2529 3.006323 CCACTGCTATGTCATACTCCCTC 59.994 52.174 0.00 0.00 0.00 4.30
2437 2530 3.006323 CACTGCTATGTCATACTCCCTCC 59.994 52.174 0.00 0.00 0.00 4.30
2438 2531 2.230025 CTGCTATGTCATACTCCCTCCG 59.770 54.545 0.00 0.00 0.00 4.63
2439 2532 2.240279 GCTATGTCATACTCCCTCCGT 58.760 52.381 0.00 0.00 0.00 4.69
2440 2533 2.628657 GCTATGTCATACTCCCTCCGTT 59.371 50.000 0.00 0.00 0.00 4.44
2441 2534 3.305471 GCTATGTCATACTCCCTCCGTTC 60.305 52.174 0.00 0.00 0.00 3.95
2442 2535 1.481871 TGTCATACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2443 2536 1.272816 TGTCATACTCCCTCCGTTCCA 60.273 52.381 0.00 0.00 0.00 3.53
2444 2537 1.829222 GTCATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
2445 2538 2.235402 GTCATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
2446 2539 2.907696 TCATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
2447 2540 3.521937 TCATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
2448 2541 4.717778 TCATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
2449 2542 5.368523 TCATACTCCCTCCGTTCCAAAATAT 59.631 40.000 0.00 0.00 0.00 1.28
2450 2543 6.555738 TCATACTCCCTCCGTTCCAAAATATA 59.444 38.462 0.00 0.00 0.00 0.86
2451 2544 5.291905 ACTCCCTCCGTTCCAAAATATAG 57.708 43.478 0.00 0.00 0.00 1.31
2452 2545 4.065789 CTCCCTCCGTTCCAAAATATAGC 58.934 47.826 0.00 0.00 0.00 2.97
2453 2546 2.806244 CCCTCCGTTCCAAAATATAGCG 59.194 50.000 0.00 0.00 0.00 4.26
2454 2547 2.223377 CCTCCGTTCCAAAATATAGCGC 59.777 50.000 0.00 0.00 0.00 5.92
2455 2548 1.862201 TCCGTTCCAAAATATAGCGCG 59.138 47.619 0.00 0.00 0.00 6.86
2456 2549 1.658968 CGTTCCAAAATATAGCGCGC 58.341 50.000 26.66 26.66 0.00 6.86
2457 2550 1.659211 CGTTCCAAAATATAGCGCGCC 60.659 52.381 30.33 10.31 0.00 6.53
2458 2551 0.948678 TTCCAAAATATAGCGCGCCC 59.051 50.000 30.33 0.16 0.00 6.13
2459 2552 0.179043 TCCAAAATATAGCGCGCCCA 60.179 50.000 30.33 17.44 0.00 5.36
2460 2553 0.040425 CCAAAATATAGCGCGCCCAC 60.040 55.000 30.33 0.00 0.00 4.61
2461 2554 0.384230 CAAAATATAGCGCGCCCACG 60.384 55.000 30.33 4.40 44.07 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.364149 AGCTGATCAATCTCTGAAATCTACT 57.636 36.000 0.00 0.00 37.67 2.57
1 2 7.041916 CCAAGCTGATCAATCTCTGAAATCTAC 60.042 40.741 0.00 0.00 37.67 2.59
2 3 6.990939 CCAAGCTGATCAATCTCTGAAATCTA 59.009 38.462 0.00 0.00 37.67 1.98
3 4 5.823570 CCAAGCTGATCAATCTCTGAAATCT 59.176 40.000 0.00 0.00 37.67 2.40
4 5 5.505985 GCCAAGCTGATCAATCTCTGAAATC 60.506 44.000 0.00 0.00 37.67 2.17
5 6 4.338682 GCCAAGCTGATCAATCTCTGAAAT 59.661 41.667 0.00 0.00 37.67 2.17
6 7 3.693085 GCCAAGCTGATCAATCTCTGAAA 59.307 43.478 0.00 0.00 37.67 2.69
7 8 3.054582 AGCCAAGCTGATCAATCTCTGAA 60.055 43.478 0.00 0.00 37.57 3.02
8 9 2.504585 AGCCAAGCTGATCAATCTCTGA 59.495 45.455 0.00 0.00 37.57 3.27
9 10 2.920524 AGCCAAGCTGATCAATCTCTG 58.079 47.619 0.00 0.00 37.57 3.35
10 11 4.978438 ATAGCCAAGCTGATCAATCTCT 57.022 40.909 0.00 0.00 40.10 3.10
11 12 5.638657 CAGTATAGCCAAGCTGATCAATCTC 59.361 44.000 0.00 0.00 40.10 2.75
12 13 5.549347 CAGTATAGCCAAGCTGATCAATCT 58.451 41.667 0.00 0.00 40.10 2.40
13 14 4.153835 GCAGTATAGCCAAGCTGATCAATC 59.846 45.833 0.00 0.00 40.10 2.67
14 15 4.070716 GCAGTATAGCCAAGCTGATCAAT 58.929 43.478 0.00 0.00 40.10 2.57
15 16 3.470709 GCAGTATAGCCAAGCTGATCAA 58.529 45.455 0.00 0.00 40.10 2.57
16 17 3.117491 GCAGTATAGCCAAGCTGATCA 57.883 47.619 0.00 0.00 40.10 2.92
27 28 4.640855 TCGCCGCGGCAGTATAGC 62.641 66.667 45.26 19.69 42.06 2.97
28 29 2.402282 TTCTCGCCGCGGCAGTATAG 62.402 60.000 45.26 31.62 42.06 1.31
29 30 1.802337 ATTCTCGCCGCGGCAGTATA 61.802 55.000 45.26 27.67 42.06 1.47
30 31 1.802337 TATTCTCGCCGCGGCAGTAT 61.802 55.000 45.26 35.57 42.06 2.12
31 32 1.802337 ATATTCTCGCCGCGGCAGTA 61.802 55.000 45.26 32.78 42.06 2.74
32 33 2.644555 AATATTCTCGCCGCGGCAGT 62.645 55.000 45.26 27.33 42.06 4.40
33 34 1.956170 AATATTCTCGCCGCGGCAG 60.956 57.895 45.26 37.32 42.06 4.85
34 35 2.108157 AATATTCTCGCCGCGGCA 59.892 55.556 45.26 31.41 42.06 5.69
35 36 2.551270 CAATATTCTCGCCGCGGC 59.449 61.111 39.82 39.82 37.85 6.53
36 37 1.594293 ACCAATATTCTCGCCGCGG 60.594 57.895 24.05 24.05 0.00 6.46
37 38 1.564622 CACCAATATTCTCGCCGCG 59.435 57.895 6.39 6.39 0.00 6.46
38 39 1.279840 GCACCAATATTCTCGCCGC 59.720 57.895 0.00 0.00 0.00 6.53
39 40 0.583438 CTGCACCAATATTCTCGCCG 59.417 55.000 0.00 0.00 0.00 6.46
40 41 1.668419 ACTGCACCAATATTCTCGCC 58.332 50.000 0.00 0.00 0.00 5.54
41 42 2.285834 CGAACTGCACCAATATTCTCGC 60.286 50.000 0.00 0.00 0.00 5.03
42 43 2.285220 CCGAACTGCACCAATATTCTCG 59.715 50.000 0.00 0.00 0.00 4.04
43 44 2.614057 CCCGAACTGCACCAATATTCTC 59.386 50.000 0.00 0.00 0.00 2.87
44 45 2.643551 CCCGAACTGCACCAATATTCT 58.356 47.619 0.00 0.00 0.00 2.40
45 46 1.676006 CCCCGAACTGCACCAATATTC 59.324 52.381 0.00 0.00 0.00 1.75
46 47 1.005450 ACCCCGAACTGCACCAATATT 59.995 47.619 0.00 0.00 0.00 1.28
47 48 0.623723 ACCCCGAACTGCACCAATAT 59.376 50.000 0.00 0.00 0.00 1.28
48 49 0.322098 CACCCCGAACTGCACCAATA 60.322 55.000 0.00 0.00 0.00 1.90
49 50 1.603455 CACCCCGAACTGCACCAAT 60.603 57.895 0.00 0.00 0.00 3.16
50 51 2.203280 CACCCCGAACTGCACCAA 60.203 61.111 0.00 0.00 0.00 3.67
51 52 4.947147 GCACCCCGAACTGCACCA 62.947 66.667 0.00 0.00 33.31 4.17
69 70 4.479993 AGGTGAGCGAGCCATGGC 62.480 66.667 30.12 30.12 42.33 4.40
70 71 2.513204 CAGGTGAGCGAGCCATGG 60.513 66.667 7.63 7.63 0.00 3.66
71 72 3.200593 GCAGGTGAGCGAGCCATG 61.201 66.667 0.00 0.00 0.00 3.66
72 73 3.382803 GAGCAGGTGAGCGAGCCAT 62.383 63.158 0.00 0.00 40.15 4.40
73 74 4.074526 GAGCAGGTGAGCGAGCCA 62.075 66.667 0.00 0.00 40.15 4.75
74 75 4.828925 GGAGCAGGTGAGCGAGCC 62.829 72.222 0.00 0.00 40.15 4.70
75 76 4.828925 GGGAGCAGGTGAGCGAGC 62.829 72.222 0.00 0.00 40.15 5.03
76 77 4.154347 GGGGAGCAGGTGAGCGAG 62.154 72.222 0.00 0.00 40.15 5.03
79 80 3.959991 GAACGGGGAGCAGGTGAGC 62.960 68.421 0.00 0.00 0.00 4.26
84 85 2.107141 GATCGAACGGGGAGCAGG 59.893 66.667 0.00 0.00 0.00 4.85
94 95 0.391263 AGGGCTGAAACCGATCGAAC 60.391 55.000 18.66 5.33 0.00 3.95
97 98 2.464459 GCAGGGCTGAAACCGATCG 61.464 63.158 8.51 8.51 0.00 3.69
122 124 2.493675 TCCGATCCAGTTTCAGAGTCAG 59.506 50.000 0.00 0.00 0.00 3.51
173 175 1.355210 CGTGTGGTGGCACTGAAAC 59.645 57.895 18.45 11.28 37.24 2.78
213 215 0.953471 TTTCTTGGCGGACGTCATGG 60.953 55.000 18.91 7.01 0.00 3.66
236 238 1.153469 CCGCCTGAGCTTCTTCTCC 60.153 63.158 0.00 0.00 36.60 3.71
238 240 2.267324 GCCGCCTGAGCTTCTTCT 59.733 61.111 0.00 0.00 36.60 2.85
239 241 2.821810 GGCCGCCTGAGCTTCTTC 60.822 66.667 0.71 0.00 36.60 2.87
240 242 4.767255 CGGCCGCCTGAGCTTCTT 62.767 66.667 14.67 0.00 36.60 2.52
261 263 0.527817 GATGGAAGACGCGTGGGTAG 60.528 60.000 20.70 0.00 0.00 3.18
262 264 0.968901 AGATGGAAGACGCGTGGGTA 60.969 55.000 20.70 0.00 0.00 3.69
263 265 2.264794 GATGGAAGACGCGTGGGT 59.735 61.111 20.70 0.00 0.00 4.51
264 266 1.811266 CAGATGGAAGACGCGTGGG 60.811 63.158 20.70 0.00 0.00 4.61
286 288 2.130272 GGGTTTCCCTTCAGTGGATC 57.870 55.000 0.00 0.00 41.34 3.36
299 301 0.526211 GCTCCACATTTCGGGGTTTC 59.474 55.000 0.00 0.00 0.00 2.78
301 303 0.893727 GTGCTCCACATTTCGGGGTT 60.894 55.000 0.00 0.00 34.08 4.11
349 351 4.559063 CCATCTGGGGAGCTGCGG 62.559 72.222 0.00 0.00 0.00 5.69
350 352 2.335092 AATCCATCTGGGGAGCTGCG 62.335 60.000 0.00 0.00 41.08 5.18
357 359 4.098501 GTGCTTAGAAAAATCCATCTGGGG 59.901 45.833 0.00 0.00 37.22 4.96
441 457 5.992217 GCATCGGTCATATATAATTCCTCCC 59.008 44.000 0.00 0.00 0.00 4.30
461 480 4.408821 TGGGCGTCAGTGGGCATC 62.409 66.667 8.92 2.42 0.00 3.91
565 584 0.098200 GCTCCGTGGCCGTATTTTTC 59.902 55.000 0.00 0.00 0.00 2.29
686 713 1.452833 GTCTGAGCAATCAGGGGGC 60.453 63.158 5.48 0.00 38.23 5.80
709 736 2.629763 CGCGCCGCCTTTTATACC 59.370 61.111 2.28 0.00 0.00 2.73
755 788 1.077930 GCAGCAGATGGAAGGCAGA 60.078 57.895 0.00 0.00 0.00 4.26
779 820 4.228567 TGGACTCGCGGTGTTGCA 62.229 61.111 6.13 0.00 34.15 4.08
780 821 3.712881 GTGGACTCGCGGTGTTGC 61.713 66.667 6.13 0.00 0.00 4.17
781 822 1.885388 TTGTGGACTCGCGGTGTTG 60.885 57.895 6.13 0.00 0.00 3.33
796 837 3.209097 GGTGGTGCTGTGCGTTGT 61.209 61.111 0.00 0.00 0.00 3.32
856 905 1.451936 GAGGCAGGGCGTATGGATT 59.548 57.895 0.00 0.00 0.00 3.01
920 976 1.007387 CAAGAAAACACAGGCCGGC 60.007 57.895 21.18 21.18 0.00 6.13
921 977 1.659794 CCAAGAAAACACAGGCCGG 59.340 57.895 0.00 0.00 0.00 6.13
922 978 1.659794 CCCAAGAAAACACAGGCCG 59.340 57.895 0.00 0.00 0.00 6.13
934 990 1.153249 CGCCTAAATCCGCCCAAGA 60.153 57.895 0.00 0.00 0.00 3.02
935 991 2.186826 CCGCCTAAATCCGCCCAAG 61.187 63.158 0.00 0.00 0.00 3.61
1227 1284 3.683281 GCGATCGATCCCTATCTAGTCCT 60.683 52.174 21.57 0.00 0.00 3.85
1278 1335 3.545366 AATTAGGAAGCTCCTCGAACC 57.455 47.619 7.85 0.00 45.66 3.62
1300 1379 2.170166 TCAAAGCTTAGCAACCATGGG 58.830 47.619 18.09 0.00 0.00 4.00
1490 1569 0.522705 CAGCATGCGATTCAGTGCAC 60.523 55.000 13.01 9.40 45.07 4.57
1582 1661 0.601311 GGCACACACACCAGAGAGAC 60.601 60.000 0.00 0.00 0.00 3.36
1583 1662 1.748403 GGCACACACACCAGAGAGA 59.252 57.895 0.00 0.00 0.00 3.10
1584 1663 1.302033 GGGCACACACACCAGAGAG 60.302 63.158 0.00 0.00 0.00 3.20
1585 1664 2.828868 GGGCACACACACCAGAGA 59.171 61.111 0.00 0.00 0.00 3.10
1711 1793 2.032528 TGGTGGTACTGCTGCTGC 59.967 61.111 8.89 8.89 40.20 5.25
1721 1806 3.943691 GCCGTGGTGGTGGTGGTA 61.944 66.667 0.00 0.00 41.21 3.25
1813 1898 3.564027 GGCGACGGCTGCATGTAC 61.564 66.667 15.00 0.00 39.81 2.90
1923 2008 0.429736 CGCGTTGACGTTGTAGTGAG 59.570 55.000 0.00 0.00 42.22 3.51
2053 2138 3.068691 TCCGCCTGGGAGAAGTCG 61.069 66.667 0.00 0.00 40.94 4.18
2430 2523 4.065789 GCTATATTTTGGAACGGAGGGAG 58.934 47.826 0.00 0.00 0.00 4.30
2431 2524 3.493699 CGCTATATTTTGGAACGGAGGGA 60.494 47.826 0.00 0.00 0.00 4.20
2432 2525 2.806244 CGCTATATTTTGGAACGGAGGG 59.194 50.000 0.00 0.00 0.00 4.30
2433 2526 2.223377 GCGCTATATTTTGGAACGGAGG 59.777 50.000 0.00 0.00 0.00 4.30
2434 2527 2.096909 CGCGCTATATTTTGGAACGGAG 60.097 50.000 5.56 0.00 0.00 4.63
2435 2528 1.862201 CGCGCTATATTTTGGAACGGA 59.138 47.619 5.56 0.00 0.00 4.69
2436 2529 1.659211 GCGCGCTATATTTTGGAACGG 60.659 52.381 26.67 0.00 0.00 4.44
2437 2530 1.658968 GCGCGCTATATTTTGGAACG 58.341 50.000 26.67 0.00 0.00 3.95
2438 2531 1.334689 GGGCGCGCTATATTTTGGAAC 60.335 52.381 32.29 8.93 0.00 3.62
2439 2532 0.948678 GGGCGCGCTATATTTTGGAA 59.051 50.000 32.29 0.00 0.00 3.53
2440 2533 0.179043 TGGGCGCGCTATATTTTGGA 60.179 50.000 32.29 0.00 0.00 3.53
2441 2534 0.040425 GTGGGCGCGCTATATTTTGG 60.040 55.000 32.29 0.00 0.00 3.28
2442 2535 0.384230 CGTGGGCGCGCTATATTTTG 60.384 55.000 32.29 9.06 0.00 2.44
2443 2536 1.938861 CGTGGGCGCGCTATATTTT 59.061 52.632 32.29 0.00 0.00 1.82
2444 2537 3.637714 CGTGGGCGCGCTATATTT 58.362 55.556 32.29 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.