Multiple sequence alignment - TraesCS2B01G095200

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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 TraesCS2B01G095200 chr2B 100.000 3896 0 0 1 3896 55211199 55207304 0.000000e+00 7195.0
1 TraesCS2B01G095200 chr2B 85.929 2267 159 54 1350 3523 55514206 55512007 0.000000e+00 2272.0
2 TraesCS2B01G095200 chr2B 87.343 1193 81 31 780 1930 55227659 55226495 0.000000e+00 1303.0
3 TraesCS2B01G095200 chr2B 86.778 1142 79 37 822 1938 55699399 55698305 0.000000e+00 1206.0
4 TraesCS2B01G095200 chr2B 86.791 1128 71 40 861 1931 55855927 55854821 0.000000e+00 1186.0
5 TraesCS2B01G095200 chr2B 89.294 906 80 9 2626 3524 55697529 55696634 0.000000e+00 1120.0
6 TraesCS2B01G095200 chr2B 93.566 746 29 4 1 740 55700254 55699522 0.000000e+00 1094.0
7 TraesCS2B01G095200 chr2B 92.358 759 43 12 2362 3111 55202170 55201418 0.000000e+00 1066.0
8 TraesCS2B01G095200 chr2B 90.945 508 39 5 1 508 55538112 55537612 0.000000e+00 676.0
9 TraesCS2B01G095200 chr2B 87.433 557 45 13 814 1355 55537037 55536491 5.530000e-173 617.0
10 TraesCS2B01G095200 chr2B 85.476 599 57 17 2571 3143 55224725 55224131 7.210000e-167 597.0
11 TraesCS2B01G095200 chr2B 88.162 321 20 6 3582 3896 55698226 55697918 2.210000e-97 366.0
12 TraesCS2B01G095200 chr2B 89.273 289 17 7 864 1151 54888293 54888018 2.230000e-92 350.0
13 TraesCS2B01G095200 chr2B 88.215 297 26 6 864 1159 55032781 55032493 2.880000e-91 346.0
14 TraesCS2B01G095200 chr2B 85.522 297 40 1 1655 1948 54786570 54786274 1.360000e-79 307.0
15 TraesCS2B01G095200 chr2B 88.302 265 17 6 2078 2329 693564059 693564322 4.890000e-79 305.0
16 TraesCS2B01G095200 chr2B 90.187 214 7 6 2096 2296 55202389 55202177 2.310000e-67 267.0
17 TraesCS2B01G095200 chr2B 80.882 340 57 5 1648 1983 122993405 122993740 1.070000e-65 261.0
18 TraesCS2B01G095200 chr2B 92.121 165 13 0 2370 2534 693564319 693564483 2.340000e-57 233.0
19 TraesCS2B01G095200 chr2B 99.180 122 1 0 2078 2199 737566649 737566770 1.820000e-53 220.0
20 TraesCS2B01G095200 chr2B 92.248 129 8 2 3601 3728 55854720 55854593 8.600000e-42 182.0
21 TraesCS2B01G095200 chr2B 88.571 140 7 4 780 918 55537317 55537186 1.120000e-35 161.0
22 TraesCS2B01G095200 chr2B 83.077 195 11 9 3535 3728 55226436 55226263 1.450000e-34 158.0
23 TraesCS2B01G095200 chr2B 94.521 73 4 0 3823 3895 55208841 55208769 3.180000e-21 113.0
24 TraesCS2B01G095200 chr2B 100.000 60 0 0 3750 3809 55854599 55854540 1.140000e-20 111.0
25 TraesCS2B01G095200 chr2B 83.871 93 12 3 3604 3695 55202354 55202264 6.940000e-13 86.1
26 TraesCS2B01G095200 chr2A 86.695 1631 101 53 780 2329 36392811 36391216 0.000000e+00 1703.0
27 TraesCS2B01G095200 chr2A 88.489 1251 98 24 2314 3524 36398909 36397665 0.000000e+00 1471.0
28 TraesCS2B01G095200 chr2A 87.552 1205 88 28 774 1943 36411938 36410761 0.000000e+00 1338.0
29 TraesCS2B01G095200 chr2A 86.031 1174 101 36 861 1985 36400210 36399051 0.000000e+00 1201.0
30 TraesCS2B01G095200 chr2A 90.186 805 58 11 2370 3169 36391219 36390431 0.000000e+00 1029.0
31 TraesCS2B01G095200 chr2A 84.733 524 55 14 2570 3074 36410240 36409723 5.810000e-138 501.0
32 TraesCS2B01G095200 chr2A 92.803 264 14 2 3634 3896 36410700 36410441 1.020000e-100 377.0
33 TraesCS2B01G095200 chr2A 85.425 247 34 2 1703 1948 36189897 36189652 5.000000e-64 255.0
34 TraesCS2B01G095200 chr2A 79.825 228 33 13 3601 3818 36234293 36234069 1.870000e-33 154.0
35 TraesCS2B01G095200 chr2A 80.090 221 25 14 3601 3815 1212104 1212311 3.140000e-31 147.0
36 TraesCS2B01G095200 chr2A 86.364 88 8 3 3531 3616 36391544 36391459 4.140000e-15 93.5
37 TraesCS2B01G095200 chr2D 88.123 1103 77 33 861 1943 33581160 33580092 0.000000e+00 1262.0
38 TraesCS2B01G095200 chr2D 85.334 1166 97 39 861 1970 33242152 33241005 0.000000e+00 1138.0
39 TraesCS2B01G095200 chr2D 84.239 1123 100 32 2054 3169 33314214 33313162 0.000000e+00 1022.0
40 TraesCS2B01G095200 chr2D 91.201 716 45 10 3155 3867 33240498 33239798 0.000000e+00 957.0
41 TraesCS2B01G095200 chr2D 88.625 800 40 18 1165 1938 33373920 33373146 0.000000e+00 926.0
42 TraesCS2B01G095200 chr2D 84.437 906 47 27 774 1623 33315546 33314679 0.000000e+00 806.0
43 TraesCS2B01G095200 chr2D 89.430 596 48 7 2743 3333 33579247 33578662 0.000000e+00 737.0
44 TraesCS2B01G095200 chr2D 88.402 388 26 8 1624 1993 33314609 33314223 2.130000e-122 449.0
45 TraesCS2B01G095200 chr2D 93.380 287 3 6 1997 2267 33241008 33240722 1.010000e-110 411.0
46 TraesCS2B01G095200 chr2D 81.911 492 51 24 2037 2517 33371876 33371412 7.900000e-102 381.0
47 TraesCS2B01G095200 chr2D 89.170 277 16 5 3634 3896 33580031 33579755 2.240000e-87 333.0
48 TraesCS2B01G095200 chr2D 81.232 341 56 5 1647 1983 79086086 79086422 6.420000e-68 268.0
49 TraesCS2B01G095200 chr2D 93.820 178 9 2 2370 2546 33240673 33240497 2.310000e-67 267.0
50 TraesCS2B01G095200 chr2D 89.941 169 7 4 3535 3695 33371887 33371721 3.940000e-50 209.0
51 TraesCS2B01G095200 chr2D 93.548 124 7 1 3773 3896 33372902 33372780 2.390000e-42 183.0
52 TraesCS2B01G095200 chr2D 90.541 74 4 1 3823 3896 33371567 33371497 1.150000e-15 95.3
53 TraesCS2B01G095200 chr2D 91.935 62 4 1 3635 3695 33240842 33240781 6.940000e-13 86.1
54 TraesCS2B01G095200 chr2D 76.923 156 23 10 3563 3715 33314209 33314064 4.170000e-10 76.8
55 TraesCS2B01G095200 chr2D 97.561 41 1 0 1988 2028 33371905 33371865 1.940000e-08 71.3
56 TraesCS2B01G095200 chr7A 82.927 656 81 19 833 1468 78080843 78080199 2.630000e-156 562.0
57 TraesCS2B01G095200 chr7A 82.016 645 86 20 914 1543 77731779 77732408 4.460000e-144 521.0
58 TraesCS2B01G095200 chr7B 82.889 637 78 18 914 1543 15935348 15935960 9.520000e-151 544.0
59 TraesCS2B01G095200 chr1B 90.476 252 19 4 2078 2329 76377278 76377524 1.040000e-85 327.0
60 TraesCS2B01G095200 chr4B 89.057 265 15 7 2078 2329 217280498 217280761 2.260000e-82 316.0
61 TraesCS2B01G095200 chr4B 91.515 165 14 0 2370 2534 217280758 217280922 1.090000e-55 228.0
62 TraesCS2B01G095200 chr4B 95.455 132 6 0 2078 2209 97763535 97763404 1.100000e-50 211.0
63 TraesCS2B01G095200 chr4A 87.925 265 18 6 2078 2329 723917743 723917480 2.280000e-77 300.0
64 TraesCS2B01G095200 chr6B 92.216 167 8 3 2078 2239 577618138 577618304 8.420000e-57 231.0
65 TraesCS2B01G095200 chr5B 89.655 174 4 6 2080 2239 61757435 61757608 3.940000e-50 209.0
66 TraesCS2B01G095200 chr3B 93.182 132 9 0 2078 2209 707598136 707598005 1.100000e-45 195.0
67 TraesCS2B01G095200 chr7D 79.911 224 26 14 3601 3818 239730639 239730429 3.140000e-31 147.0
68 TraesCS2B01G095200 chr7D 82.911 158 12 6 3618 3760 190392012 190391855 1.140000e-25 128.0
69 TraesCS2B01G095200 chr5A 79.018 224 28 14 3601 3818 565537305 565537095 6.790000e-28 135.0
70 TraesCS2B01G095200 chrUn 80.303 198 21 12 2131 2311 76849336 76849532 2.440000e-27 134.0
71 TraesCS2B01G095200 chr6D 81.250 176 19 8 2150 2311 31638483 31638658 3.160000e-26 130.0
72 TraesCS2B01G095200 chr3A 81.579 114 7 4 3661 3760 167344191 167344304 8.970000e-12 82.4


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 TraesCS2B01G095200 chr2B 55207304 55211199 3895 True 3654.000000 7195 97.260500 1 3896 2 chr2B.!!$R6 3895
1 TraesCS2B01G095200 chr2B 55512007 55514206 2199 True 2272.000000 2272 85.929000 1350 3523 1 chr2B.!!$R4 2173
2 TraesCS2B01G095200 chr2B 55696634 55700254 3620 True 946.500000 1206 89.450000 1 3896 4 chr2B.!!$R9 3895
3 TraesCS2B01G095200 chr2B 55224131 55227659 3528 True 686.000000 1303 85.298667 780 3728 3 chr2B.!!$R7 2948
4 TraesCS2B01G095200 chr2B 55854540 55855927 1387 True 493.000000 1186 93.013000 861 3809 3 chr2B.!!$R10 2948
5 TraesCS2B01G095200 chr2B 55536491 55538112 1621 True 484.666667 676 88.983000 1 1355 3 chr2B.!!$R8 1354
6 TraesCS2B01G095200 chr2B 55201418 55202389 971 True 473.033333 1066 88.805333 2096 3695 3 chr2B.!!$R5 1599
7 TraesCS2B01G095200 chr2A 36397665 36400210 2545 True 1336.000000 1471 87.260000 861 3524 2 chr2A.!!$R4 2663
8 TraesCS2B01G095200 chr2A 36390431 36392811 2380 True 941.833333 1703 87.748333 780 3616 3 chr2A.!!$R3 2836
9 TraesCS2B01G095200 chr2A 36409723 36411938 2215 True 738.666667 1338 88.362667 774 3896 3 chr2A.!!$R5 3122
10 TraesCS2B01G095200 chr2D 33578662 33581160 2498 True 777.333333 1262 88.907667 861 3896 3 chr2D.!!$R4 3035
11 TraesCS2B01G095200 chr2D 33313162 33315546 2384 True 588.450000 1022 83.500250 774 3715 4 chr2D.!!$R2 2941
12 TraesCS2B01G095200 chr2D 33239798 33242152 2354 True 571.820000 1138 91.134000 861 3867 5 chr2D.!!$R1 3006
13 TraesCS2B01G095200 chr2D 33371412 33373920 2508 True 310.933333 926 90.354500 1165 3896 6 chr2D.!!$R3 2731
14 TraesCS2B01G095200 chr7A 78080199 78080843 644 True 562.000000 562 82.927000 833 1468 1 chr7A.!!$R1 635
15 TraesCS2B01G095200 chr7A 77731779 77732408 629 False 521.000000 521 82.016000 914 1543 1 chr7A.!!$F1 629
16 TraesCS2B01G095200 chr7B 15935348 15935960 612 False 544.000000 544 82.889000 914 1543 1 chr7B.!!$F1 629

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
768 840 0.544357 TTCCTCCATGGGACTCGTGT 60.544 55.0 13.02 0.0 34.78 4.49 F
1618 2173 0.605083 TGTGATTCGACTGCAGCTCT 59.395 50.0 15.27 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2381 1.155889 GACGCACATGGTGATGTTCA 58.844 50.000 0.00 0.0 41.12 3.18 R
3493 5737 1.143073 GAACCTGTGGGAAGTTCCAGT 59.857 52.381 23.33 9.2 38.64 4.00 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
82 83 4.040829 AGCTTTGCTAAAAGGCCTTTGATT 59.959 37.500 31.02 18.06 42.66 2.57
216 217 3.120442 CGGGTCTTAACCTAAAACAAGCG 60.120 47.826 0.00 0.00 45.66 4.68
242 243 3.853307 GCAAAAACTCACATCAAGGACGG 60.853 47.826 0.00 0.00 0.00 4.79
267 268 6.144854 CGTCAATTGAAGATTGAAGAAGCAA 58.855 36.000 15.34 0.00 38.97 3.91
383 384 4.953940 ACCCAAGCTAGAGATGAAGATC 57.046 45.455 0.00 0.00 0.00 2.75
397 398 5.998981 AGATGAAGATCCGTCGTACTCTAAT 59.001 40.000 0.00 0.00 0.00 1.73
401 402 3.819902 AGATCCGTCGTACTCTAATTCCC 59.180 47.826 0.00 0.00 0.00 3.97
502 509 1.378382 CATGGGTCCACGCCATGAA 60.378 57.895 12.19 0.00 42.33 2.57
543 550 9.520515 ACCATTCTAGAATAAAAACACACTCAT 57.479 29.630 17.53 0.00 0.00 2.90
558 565 4.925646 CACACTCATCATGTATATCCACGG 59.074 45.833 0.00 0.00 0.00 4.94
577 584 3.172050 CGGCCTCTTCGACATATTATCG 58.828 50.000 0.00 0.50 41.00 2.92
624 631 4.988540 CGACACCGACCAATCAATATGTAT 59.011 41.667 0.00 0.00 38.22 2.29
640 647 8.655901 TCAATATGTATGTGGAATAGGTAAGCA 58.344 33.333 0.00 0.00 0.00 3.91
644 651 7.368198 TGTATGTGGAATAGGTAAGCACATA 57.632 36.000 0.00 0.00 34.28 2.29
768 840 0.544357 TTCCTCCATGGGACTCGTGT 60.544 55.000 13.02 0.00 34.78 4.49
769 841 0.970937 TCCTCCATGGGACTCGTGTC 60.971 60.000 13.02 9.11 42.22 3.67
778 858 0.674534 GGACTCGTGTCAACAGAGGT 59.325 55.000 18.45 0.32 44.61 3.85
1446 1876 2.092753 CAGCTCCATGATGTACTGGGTT 60.093 50.000 0.00 0.00 33.13 4.11
1470 1900 3.866582 CCCATCCCCGCCAGAGAC 61.867 72.222 0.00 0.00 0.00 3.36
1471 1901 3.866582 CCATCCCCGCCAGAGACC 61.867 72.222 0.00 0.00 0.00 3.85
1472 1902 4.227134 CATCCCCGCCAGAGACCG 62.227 72.222 0.00 0.00 0.00 4.79
1485 1915 3.134127 GACCGCTGGAACATGCCC 61.134 66.667 0.00 0.00 38.20 5.36
1486 1916 3.628646 GACCGCTGGAACATGCCCT 62.629 63.158 6.33 0.00 38.20 5.19
1487 1917 2.361610 CCGCTGGAACATGCCCTT 60.362 61.111 6.33 0.00 38.20 3.95
1496 1926 1.004745 GAACATGCCCTTCCTTCCTGA 59.995 52.381 0.00 0.00 0.00 3.86
1528 1969 2.227089 GAGTTCGCCATGACCGACCT 62.227 60.000 7.75 6.70 34.01 3.85
1545 2002 3.669023 CGACCTGCTTCTTGAATTGCTTC 60.669 47.826 0.00 0.00 0.00 3.86
1600 2155 7.424227 AGTTCAATTATGTTGTTGCCAAATG 57.576 32.000 0.00 0.00 30.94 2.32
1616 2171 2.105006 AATGTGATTCGACTGCAGCT 57.895 45.000 15.27 0.23 0.00 4.24
1617 2172 1.649664 ATGTGATTCGACTGCAGCTC 58.350 50.000 15.27 9.81 0.00 4.09
1618 2173 0.605083 TGTGATTCGACTGCAGCTCT 59.395 50.000 15.27 0.00 0.00 4.09
1619 2174 1.001293 TGTGATTCGACTGCAGCTCTT 59.999 47.619 15.27 0.00 0.00 2.85
1620 2175 1.392853 GTGATTCGACTGCAGCTCTTG 59.607 52.381 15.27 0.00 0.00 3.02
1621 2176 1.273327 TGATTCGACTGCAGCTCTTGA 59.727 47.619 15.27 0.51 0.00 3.02
1622 2177 2.093816 TGATTCGACTGCAGCTCTTGAT 60.094 45.455 15.27 0.33 0.00 2.57
1799 2381 3.818787 CGCCGGCGTGTACTACCT 61.819 66.667 39.71 0.00 34.35 3.08
1807 2389 2.094390 GGCGTGTACTACCTGAACATCA 60.094 50.000 0.00 0.00 0.00 3.07
1858 2440 3.220999 CTGACCCCGCTCGTTGTCA 62.221 63.158 9.59 9.59 36.40 3.58
1952 2539 1.380380 CTCCATGCCCCAACTTCCC 60.380 63.158 0.00 0.00 0.00 3.97
1961 2554 2.945890 GCCCCAACTTCCCAAGTATCTG 60.946 54.545 0.00 0.00 41.91 2.90
2350 4060 7.032580 CCAATTTTACTCGCATTGAATAACCA 58.967 34.615 0.00 0.00 30.66 3.67
2431 4151 4.685169 ATTCAGGTTTTGTACATGAGCG 57.315 40.909 0.00 0.00 46.97 5.03
2697 4855 7.907214 TTTTACCTTTGCAGAGAAGATACTC 57.093 36.000 5.68 0.00 37.19 2.59
2904 5086 2.543012 CGACGCGGAGTAGAGAAAGATA 59.457 50.000 12.47 0.00 0.00 1.98
2906 5090 3.806380 ACGCGGAGTAGAGAAAGATAGA 58.194 45.455 12.47 0.00 0.00 1.98
2990 5175 8.150827 TGGATGCTTATTTCTGCCTATATAGT 57.849 34.615 8.92 0.00 0.00 2.12
3123 5318 0.111089 CGTTGCAGTGTCGCTCTTTC 60.111 55.000 0.00 0.00 0.00 2.62
3197 5438 8.999220 TGCAACATTTTTAGATTATGCATTCA 57.001 26.923 3.54 0.00 37.61 2.57
3408 5651 2.023673 TCTTAATTTCCGGCCTGCATG 58.976 47.619 0.00 0.00 0.00 4.06
3424 5667 4.264253 CTGCATGTACCAGGAAGAAATGA 58.736 43.478 0.00 0.00 0.00 2.57
3465 5708 7.170998 CGAAAAGGCCTTACGATAGAATTGTAT 59.829 37.037 29.07 4.52 41.38 2.29
3510 5754 0.474184 ACACTGGAACTTCCCACAGG 59.526 55.000 5.30 0.00 35.03 4.00
3561 5805 4.334552 TCAGATTTTGGTGCAGATGCTTA 58.665 39.130 6.35 0.00 42.66 3.09
3654 5904 7.873505 AGGTTACTGAAATTGTTCTAGTCTGAC 59.126 37.037 0.00 0.00 34.60 3.51
3697 5948 7.656137 TGTTGAAGTCTGAAACTGTTAGGTATC 59.344 37.037 0.00 0.00 38.58 2.24
3719 5979 6.060028 TCTGCAACTGTTGAAATCTTGTAC 57.940 37.500 23.81 2.97 0.00 2.90
3724 5984 6.751888 GCAACTGTTGAAATCTTGTACAAGTT 59.248 34.615 29.83 21.49 39.38 2.66
3842 6150 6.432783 TCACGAAATTCAGGTTCCAACAATAT 59.567 34.615 0.00 0.00 0.00 1.28
3872 6180 1.392853 CTCGTTTCTGCACATGAGCTC 59.607 52.381 16.24 6.82 34.99 4.09
3884 6192 4.397417 GCACATGAGCTCTATTCAGGTTTT 59.603 41.667 16.19 0.00 37.46 2.43
3890 6198 5.932303 TGAGCTCTATTCAGGTTTTGTACAC 59.068 40.000 16.19 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.775854 GCAAAGCTCTATGATGTCCATATATAT 57.224 33.333 0.00 0.00 37.14 0.86
41 42 8.985922 AGCAAAGCTCTATGATGTCCATATATA 58.014 33.333 0.00 0.00 37.14 0.86
42 43 7.859540 AGCAAAGCTCTATGATGTCCATATAT 58.140 34.615 0.00 0.00 37.14 0.86
43 44 7.250032 AGCAAAGCTCTATGATGTCCATATA 57.750 36.000 0.00 0.00 37.14 0.86
163 164 3.120338 GCTACTGCTACATTTGCGTTCAA 60.120 43.478 0.00 0.00 36.03 2.69
216 217 3.803778 CCTTGATGTGAGTTTTTGCAACC 59.196 43.478 0.00 0.00 0.00 3.77
242 243 4.556523 GCTTCTTCAATCTTCAATTGACGC 59.443 41.667 7.89 0.00 37.71 5.19
267 268 5.163416 GCATGTTATACCATGGAAGGCTTTT 60.163 40.000 21.47 0.00 42.01 2.27
383 384 2.034305 CAGGGGAATTAGAGTACGACGG 59.966 54.545 0.00 0.00 0.00 4.79
397 398 1.650242 TTGTTGTGGAGCCAGGGGAA 61.650 55.000 0.00 0.00 0.00 3.97
401 402 1.331214 AATGTTGTTGTGGAGCCAGG 58.669 50.000 0.00 0.00 0.00 4.45
543 550 2.889512 AGAGGCCGTGGATATACATGA 58.110 47.619 8.87 0.00 0.00 3.07
558 565 4.416620 CTCCGATAATATGTCGAAGAGGC 58.583 47.826 11.20 0.00 41.40 4.70
577 584 1.449778 GGTGGTCGCCTTTAGCTCC 60.450 63.158 0.00 0.00 40.39 4.70
601 608 3.194861 ACATATTGATTGGTCGGTGTCG 58.805 45.455 0.00 0.00 37.82 4.35
610 617 8.868522 ACCTATTCCACATACATATTGATTGG 57.131 34.615 0.00 0.00 0.00 3.16
624 631 5.424757 GTGTATGTGCTTACCTATTCCACA 58.575 41.667 0.00 0.00 40.26 4.17
640 647 3.312421 GCATAAAGTCATGCCGTGTATGT 59.688 43.478 0.00 0.00 44.55 2.29
745 764 0.833949 GAGTCCCATGGAGGAAGGTC 59.166 60.000 15.22 0.00 41.22 3.85
746 765 0.978146 CGAGTCCCATGGAGGAAGGT 60.978 60.000 15.22 0.00 41.22 3.50
747 766 0.978146 ACGAGTCCCATGGAGGAAGG 60.978 60.000 15.22 0.00 41.22 3.46
749 768 0.544357 ACACGAGTCCCATGGAGGAA 60.544 55.000 15.22 0.00 41.22 3.36
750 769 0.970937 GACACGAGTCCCATGGAGGA 60.971 60.000 15.22 0.00 38.89 3.71
751 770 1.257750 TGACACGAGTCCCATGGAGG 61.258 60.000 15.22 0.00 44.33 4.30
752 771 0.608130 TTGACACGAGTCCCATGGAG 59.392 55.000 15.22 3.25 44.33 3.86
768 840 0.539669 TCGAGCTCCACCTCTGTTGA 60.540 55.000 8.47 0.00 0.00 3.18
769 841 0.534412 ATCGAGCTCCACCTCTGTTG 59.466 55.000 8.47 0.00 0.00 3.33
778 858 1.676678 GCCCACACTATCGAGCTCCA 61.677 60.000 8.47 0.00 0.00 3.86
856 936 0.679960 AGGTATTTCAAGGTGCCGCC 60.680 55.000 0.00 0.00 37.58 6.13
858 938 1.379527 GGAGGTATTTCAAGGTGCCG 58.620 55.000 0.00 0.00 0.00 5.69
1470 1900 2.361610 AAGGGCATGTTCCAGCGG 60.362 61.111 9.35 0.00 0.00 5.52
1471 1901 2.409870 GGAAGGGCATGTTCCAGCG 61.410 63.158 8.36 0.00 42.79 5.18
1472 1902 0.613012 AAGGAAGGGCATGTTCCAGC 60.613 55.000 14.20 4.34 45.30 4.85
1473 1903 1.467920 GAAGGAAGGGCATGTTCCAG 58.532 55.000 14.20 0.00 45.30 3.86
1474 1904 0.039618 GGAAGGAAGGGCATGTTCCA 59.960 55.000 14.20 0.00 45.30 3.53
1475 1905 0.332972 AGGAAGGAAGGGCATGTTCC 59.667 55.000 5.61 5.61 43.49 3.62
1477 1907 1.075601 TCAGGAAGGAAGGGCATGTT 58.924 50.000 0.00 0.00 0.00 2.71
1485 1915 2.245438 GAGGCGGGTCAGGAAGGAAG 62.245 65.000 0.00 0.00 0.00 3.46
1486 1916 2.203938 AGGCGGGTCAGGAAGGAA 60.204 61.111 0.00 0.00 0.00 3.36
1487 1917 2.683933 GAGGCGGGTCAGGAAGGA 60.684 66.667 0.00 0.00 0.00 3.36
1528 1969 1.541147 CCGGAAGCAATTCAAGAAGCA 59.459 47.619 0.00 0.00 0.00 3.91
1545 2002 1.154205 AGAATTCGCTCAATCGCCGG 61.154 55.000 0.00 0.00 0.00 6.13
1600 2155 1.392853 CAAGAGCTGCAGTCGAATCAC 59.607 52.381 16.64 0.00 0.00 3.06
1616 2171 2.449730 ACCCCGAGGAGGTATATCAAGA 59.550 50.000 0.00 0.00 35.24 3.02
1617 2172 2.826725 GACCCCGAGGAGGTATATCAAG 59.173 54.545 0.00 0.00 37.88 3.02
1618 2173 2.178325 TGACCCCGAGGAGGTATATCAA 59.822 50.000 0.00 0.00 37.88 2.57
1619 2174 1.784593 TGACCCCGAGGAGGTATATCA 59.215 52.381 0.00 0.00 37.88 2.15
1620 2175 2.599408 TGACCCCGAGGAGGTATATC 57.401 55.000 0.00 0.00 37.88 1.63
1621 2176 2.655407 AGATGACCCCGAGGAGGTATAT 59.345 50.000 0.00 2.12 37.88 0.86
1622 2177 2.071372 AGATGACCCCGAGGAGGTATA 58.929 52.381 0.00 0.00 37.88 1.47
1799 2381 1.155889 GACGCACATGGTGATGTTCA 58.844 50.000 0.00 0.00 41.12 3.18
1854 2436 4.308458 CCGTCGGGCAGGTTGACA 62.308 66.667 2.34 0.00 32.91 3.58
1952 2539 6.108687 TCTTGTCACCATTAGCAGATACTTG 58.891 40.000 0.00 0.00 0.00 3.16
1961 2554 5.689383 TTTCAGTTCTTGTCACCATTAGC 57.311 39.130 0.00 0.00 0.00 3.09
2203 3821 4.299586 TGCAGACAATTCCCAACAGATA 57.700 40.909 0.00 0.00 0.00 1.98
2204 3822 3.159213 TGCAGACAATTCCCAACAGAT 57.841 42.857 0.00 0.00 0.00 2.90
2350 4060 3.963129 TGGAACCTGAGTTTTGTTCACT 58.037 40.909 0.00 0.00 40.04 3.41
2431 4151 5.904362 AGAATAACAAGACCAAGATTGCC 57.096 39.130 0.00 0.00 0.00 4.52
2791 4971 8.587608 ACCAACAATCAACAACAATATCAAGAT 58.412 29.630 0.00 0.00 0.00 2.40
2805 4987 1.336240 GGCAGCAGACCAACAATCAAC 60.336 52.381 0.00 0.00 0.00 3.18
2904 5086 1.625818 AGTTTCATGACTCCCGCTTCT 59.374 47.619 0.00 0.00 0.00 2.85
2906 5090 2.224523 TGAAGTTTCATGACTCCCGCTT 60.225 45.455 0.00 0.00 31.01 4.68
3000 5185 9.050601 AGAAACAGAGAGAGTTTTTGAACATAG 57.949 33.333 0.00 0.00 39.15 2.23
3143 5338 7.896811 TCATCTACGAAGCATACCAGAAATAT 58.103 34.615 0.00 0.00 0.00 1.28
3154 5349 4.063998 TGCAAGATCATCTACGAAGCAT 57.936 40.909 0.00 0.00 0.00 3.79
3197 5438 1.888512 ACTGCATTTTCCAATGACGCT 59.111 42.857 0.00 0.00 42.35 5.07
3314 5556 6.957631 TCAGGAAAAATACTATCAAGGCAGA 58.042 36.000 0.00 0.00 0.00 4.26
3367 5610 7.462571 AAGAACTTTAAACACACAAGGAAGT 57.537 32.000 0.00 0.00 0.00 3.01
3396 5639 3.006133 TGGTACATGCAGGCCGGA 61.006 61.111 5.05 0.00 0.00 5.14
3408 5651 2.026262 TGGCCTCATTTCTTCCTGGTAC 60.026 50.000 3.32 0.00 0.00 3.34
3424 5667 2.489938 TTTCGCTTTACTCATGGCCT 57.510 45.000 3.32 0.00 0.00 5.19
3493 5737 1.143073 GAACCTGTGGGAAGTTCCAGT 59.857 52.381 23.33 9.20 38.64 4.00
3561 5805 4.140639 ACCCCCACTAAAGTAAACCCAAAT 60.141 41.667 0.00 0.00 0.00 2.32
3697 5948 5.820131 TGTACAAGATTTCAACAGTTGCAG 58.180 37.500 8.58 0.00 0.00 4.41
3719 5979 5.928264 GGGGTTTCAATTTCAGATCAACTTG 59.072 40.000 0.00 0.00 0.00 3.16
3724 5984 6.269538 TGATTTGGGGTTTCAATTTCAGATCA 59.730 34.615 0.00 0.00 0.00 2.92
3842 6150 8.726068 TCATGTGCAGAAACGAGATTTATTTAA 58.274 29.630 0.00 0.00 0.00 1.52
3872 6180 4.929808 AGCTCGTGTACAAAACCTGAATAG 59.070 41.667 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.