Multiple sequence alignment - TraesCS6A01G372200

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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 TraesCS6A01G372200 chr6A 100.000 2287 0 0 1 2287 596163871 596161585 0.000000e+00 4224.0
1 TraesCS6A01G372200 chr6A 93.137 102 6 1 1933 2034 81256988 81256888 5.090000e-32 148.0
2 TraesCS6A01G372200 chr6D 86.392 1896 147 63 393 2215 450642165 450640308 0.000000e+00 1969.0
3 TraesCS6A01G372200 chr6D 94.391 624 32 2 14 637 76079826 76080446 0.000000e+00 955.0
4 TraesCS6A01G372200 chr6B 87.322 1191 72 36 941 2093 684385650 684384501 0.000000e+00 1290.0
5 TraesCS6A01G372200 chr6B 89.421 501 39 9 5 494 684386936 684386439 8.970000e-174 619.0
6 TraesCS6A01G372200 chr6B 83.377 385 31 13 593 948 684386072 684385692 2.190000e-85 326.0
7 TraesCS6A01G372200 chr6B 88.000 125 11 3 1940 2063 713310415 713310536 6.580000e-31 145.0
8 TraesCS6A01G372200 chr6B 87.200 125 12 3 1940 2063 713517696 713517817 3.060000e-29 139.0
9 TraesCS6A01G372200 chr6B 91.089 101 8 1 1940 2039 713863976 713864076 3.960000e-28 135.0
10 TraesCS6A01G372200 chr6B 100.000 33 0 0 486 518 684386435 684386403 6.820000e-06 62.1
11 TraesCS6A01G372200 chr3D 94.822 618 29 2 20 637 382820622 382820008 0.000000e+00 961.0
12 TraesCS6A01G372200 chr3D 94.822 618 29 2 20 637 554659307 554658693 0.000000e+00 961.0
13 TraesCS6A01G372200 chr1D 94.391 624 32 2 14 637 207148126 207148746 0.000000e+00 955.0
14 TraesCS6A01G372200 chr1D 91.509 106 8 1 1702 1807 436972424 436972320 6.580000e-31 145.0
15 TraesCS6A01G372200 chr7D 95.745 188 8 0 1100 1287 84178254 84178441 1.030000e-78 303.0
16 TraesCS6A01G372200 chr7D 95.000 100 4 1 1940 2038 549548400 549548499 3.040000e-34 156.0
17 TraesCS6A01G372200 chr7B 95.213 188 9 0 1100 1287 33805426 33805613 4.780000e-77 298.0
18 TraesCS6A01G372200 chr7B 92.000 125 10 0 3 127 745863002 745863126 2.330000e-40 176.0
19 TraesCS6A01G372200 chr7B 91.339 127 11 0 3 129 745923811 745923937 8.400000e-40 174.0
20 TraesCS6A01G372200 chr7B 91.200 125 11 0 3 127 745807001 745807125 1.090000e-38 171.0
21 TraesCS6A01G372200 chr7B 88.976 127 10 1 3 129 745841014 745841136 1.090000e-33 154.0
22 TraesCS6A01G372200 chr7B 92.000 100 6 2 1940 2038 593924965 593925063 3.060000e-29 139.0
23 TraesCS6A01G372200 chr7B 92.473 93 6 1 1940 2031 285454993 285454901 5.130000e-27 132.0
24 TraesCS6A01G372200 chr7A 93.617 188 12 0 1100 1287 85588719 85588906 4.810000e-72 281.0
25 TraesCS6A01G372200 chr5B 88.281 128 10 3 1680 1807 13842016 13842138 5.090000e-32 148.0
26 TraesCS6A01G372200 chr5B 87.402 127 11 4 1681 1807 36190840 36190719 8.520000e-30 141.0
27 TraesCS6A01G372200 chr5B 86.614 127 11 5 1681 1807 13830494 13830614 3.960000e-28 135.0
28 TraesCS6A01G372200 chr5B 95.652 46 2 0 2222 2267 36797746 36797701 8.760000e-10 75.0
29 TraesCS6A01G372200 chr5B 95.652 46 2 0 2222 2267 36827745 36827700 8.760000e-10 75.0
30 TraesCS6A01G372200 chr5A 88.281 128 10 3 1680 1807 12541416 12541538 5.090000e-32 148.0
31 TraesCS6A01G372200 chr5D 90.179 112 9 2 1696 1807 17506926 17506817 6.580000e-31 145.0
32 TraesCS6A01G372200 chr5D 87.903 124 10 4 1684 1807 17855176 17855058 8.520000e-30 141.0
33 TraesCS6A01G372200 chrUn 95.652 46 2 0 2222 2267 65831375 65831420 8.760000e-10 75.0


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 TraesCS6A01G372200 chr6A 596161585 596163871 2286 True 4224.000 4224 100.000 1 2287 1 chr6A.!!$R2 2286
1 TraesCS6A01G372200 chr6D 450640308 450642165 1857 True 1969.000 1969 86.392 393 2215 1 chr6D.!!$R1 1822
2 TraesCS6A01G372200 chr6D 76079826 76080446 620 False 955.000 955 94.391 14 637 1 chr6D.!!$F1 623
3 TraesCS6A01G372200 chr6B 684384501 684386936 2435 True 574.275 1290 90.030 5 2093 4 chr6B.!!$R1 2088
4 TraesCS6A01G372200 chr3D 382820008 382820622 614 True 961.000 961 94.822 20 637 1 chr3D.!!$R1 617
5 TraesCS6A01G372200 chr3D 554658693 554659307 614 True 961.000 961 94.822 20 637 1 chr3D.!!$R2 617
6 TraesCS6A01G372200 chr1D 207148126 207148746 620 False 955.000 955 94.391 14 637 1 chr1D.!!$F1 623

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
291 295 0.463654 TTCACAGCACACAGGACCAC 60.464 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1717 0.103208 GGATCACAGCTACTGACGGG 59.897 60.0 0.78 0.0 35.18 5.28 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
46 47 1.549243 TTACCTCGCCCATGTCTGCA 61.549 55.000 0.00 0.00 0.00 4.41
78 79 3.068691 CTCCGTCTCCCGCTCCAA 61.069 66.667 0.00 0.00 34.38 3.53
145 147 3.857157 ACCTAAGTGACACACCAACAT 57.143 42.857 8.59 0.00 34.49 2.71
170 172 3.989817 CCATAAGAGCAACAAACAAAGGC 59.010 43.478 0.00 0.00 0.00 4.35
291 295 0.463654 TTCACAGCACACAGGACCAC 60.464 55.000 0.00 0.00 0.00 4.16
321 325 0.961019 GCCAGCAATTCACCAAGACA 59.039 50.000 0.00 0.00 0.00 3.41
337 347 3.032017 AGACACATGGTTTCTCTGTCG 57.968 47.619 0.00 0.00 37.03 4.35
345 355 1.192534 GGTTTCTCTGTCGAAGCAACG 59.807 52.381 0.00 0.00 0.00 4.10
384 394 0.822164 GGTACTGTGGGTGAGCGTAT 59.178 55.000 0.00 0.00 0.00 3.06
648 926 1.254026 TGTAGAATATCTCCGGCGGG 58.746 55.000 27.98 17.02 0.00 6.13
764 1052 1.192803 GGTTCTGTTCTCTCGGGGGT 61.193 60.000 0.00 0.00 0.00 4.95
784 1082 1.231928 GAGGAGGAGGGAGGAGGTC 59.768 68.421 0.00 0.00 0.00 3.85
886 1200 1.095807 GCATAACAACGGAGCCCTCC 61.096 60.000 4.19 4.19 46.18 4.30
963 1333 3.827898 CCCGAGCACTCCGTCTCC 61.828 72.222 0.00 0.00 0.00 3.71
1016 1404 1.221840 CCATGGGTAACGCTCTGCT 59.778 57.895 2.85 0.00 37.60 4.24
1024 1412 2.516048 TAACGCTCTGCTCCCCCTCT 62.516 60.000 0.00 0.00 0.00 3.69
1025 1413 3.080121 CGCTCTGCTCCCCCTCTT 61.080 66.667 0.00 0.00 0.00 2.85
1030 1418 4.760220 TGCTCCCCCTCTTCCCCC 62.760 72.222 0.00 0.00 0.00 5.40
1055 1443 4.081917 GCTAGATCCCTATCCTACTGTTGC 60.082 50.000 0.00 0.00 31.98 4.17
1063 1451 0.034337 TCCTACTGTTGCCGTGGTTC 59.966 55.000 0.00 0.00 0.00 3.62
1065 1453 1.542547 CCTACTGTTGCCGTGGTTCTT 60.543 52.381 0.00 0.00 0.00 2.52
1066 1454 1.798813 CTACTGTTGCCGTGGTTCTTC 59.201 52.381 0.00 0.00 0.00 2.87
1067 1455 0.180406 ACTGTTGCCGTGGTTCTTCT 59.820 50.000 0.00 0.00 0.00 2.85
1068 1456 1.308998 CTGTTGCCGTGGTTCTTCTT 58.691 50.000 0.00 0.00 0.00 2.52
1078 1466 1.239347 GGTTCTTCTTGGTGCTGACC 58.761 55.000 0.00 0.00 43.48 4.02
1351 1746 0.456221 AGTAGCTGTGATCCGTTCCG 59.544 55.000 0.00 0.00 0.00 4.30
1362 1757 1.523711 CCGTTCCGGTATGCATGCT 60.524 57.895 20.33 7.07 42.73 3.79
1363 1758 0.249699 CCGTTCCGGTATGCATGCTA 60.250 55.000 20.33 5.73 42.73 3.49
1364 1759 1.577468 CGTTCCGGTATGCATGCTAA 58.423 50.000 20.33 3.61 0.00 3.09
1365 1760 1.526887 CGTTCCGGTATGCATGCTAAG 59.473 52.381 20.33 5.80 0.00 2.18
1366 1761 2.801699 CGTTCCGGTATGCATGCTAAGA 60.802 50.000 20.33 6.33 0.00 2.10
1367 1762 3.202906 GTTCCGGTATGCATGCTAAGAA 58.797 45.455 20.33 11.55 0.00 2.52
1368 1763 3.111853 TCCGGTATGCATGCTAAGAAG 57.888 47.619 20.33 5.99 0.00 2.85
1509 1909 6.661377 TGGCAACCTGCTTCTGTTATTTTATA 59.339 34.615 0.00 0.00 44.28 0.98
1510 1910 7.341769 TGGCAACCTGCTTCTGTTATTTTATAT 59.658 33.333 0.00 0.00 44.28 0.86
1511 1911 7.649306 GGCAACCTGCTTCTGTTATTTTATATG 59.351 37.037 0.00 0.00 44.28 1.78
1558 1958 5.407407 ACCAGAGTACTGATTAGTGGTTG 57.593 43.478 0.00 0.00 46.03 3.77
1581 1981 4.271291 GGAACGAATCCTTAGCTGAATGAC 59.729 45.833 0.00 0.00 45.56 3.06
1602 2002 1.065491 CCAGCAATAGTGTACCAGCCA 60.065 52.381 0.00 0.00 0.00 4.75
1636 2036 3.004002 TCTTGTTGCTGATGCTTTGTCTG 59.996 43.478 0.00 0.00 40.48 3.51
1650 2050 6.042143 TGCTTTGTCTGGATTTGAAAACTTC 58.958 36.000 0.00 0.00 0.00 3.01
1652 2052 6.199719 GCTTTGTCTGGATTTGAAAACTTCTG 59.800 38.462 0.00 0.00 0.00 3.02
1653 2053 6.773976 TTGTCTGGATTTGAAAACTTCTGT 57.226 33.333 0.00 0.00 0.00 3.41
1658 2058 8.070769 GTCTGGATTTGAAAACTTCTGTACTTC 58.929 37.037 0.00 0.00 0.00 3.01
1659 2059 7.228706 TCTGGATTTGAAAACTTCTGTACTTCC 59.771 37.037 0.00 0.00 0.00 3.46
1791 2191 4.979335 TGATTTGTATGCCGATTATCCCA 58.021 39.130 0.00 0.00 0.00 4.37
1885 2295 2.113910 ATCGTTGTGCGTGTTTTTCC 57.886 45.000 0.00 0.00 42.13 3.13
1934 2355 5.936054 ACAGCTCTCTTTTTCGATTGATTG 58.064 37.500 0.00 0.00 0.00 2.67
2045 2466 4.558226 TTCTGATGATACACAACTGGCT 57.442 40.909 0.00 0.00 0.00 4.75
2049 2470 2.078849 TGATACACAACTGGCTCACG 57.921 50.000 0.00 0.00 0.00 4.35
2119 2557 9.118300 ACAGGTTTTCAATTGAAATTTTATGCA 57.882 25.926 29.13 12.74 42.83 3.96
2126 2564 8.836268 TCAATTGAAATTTTATGCAGCTTTCT 57.164 26.923 5.45 0.00 0.00 2.52
2147 2585 8.460831 TTTCTGAGCTTTTTGTCAGTTTAAAC 57.539 30.769 10.47 10.47 40.97 2.01
2148 2586 7.151999 TCTGAGCTTTTTGTCAGTTTAAACA 57.848 32.000 20.06 0.00 40.97 2.83
2149 2587 7.771183 TCTGAGCTTTTTGTCAGTTTAAACAT 58.229 30.769 20.06 3.09 40.97 2.71
2176 2626 5.930837 TTCTGTCCCATTTGACTTTTGTT 57.069 34.783 0.00 0.00 36.21 2.83
2187 2637 5.975693 TTGACTTTTGTTGGTCTGTCTTT 57.024 34.783 0.00 0.00 34.01 2.52
2194 2644 3.691575 TGTTGGTCTGTCTTTGTTGGAA 58.308 40.909 0.00 0.00 0.00 3.53
2218 2668 9.774742 GAAACTCCATTTCATTGTTGTATCTAC 57.225 33.333 0.00 0.00 45.32 2.59
2219 2669 7.865706 ACTCCATTTCATTGTTGTATCTACC 57.134 36.000 0.00 0.00 0.00 3.18
2220 2670 6.538742 ACTCCATTTCATTGTTGTATCTACCG 59.461 38.462 0.00 0.00 0.00 4.02
2221 2671 6.411376 TCCATTTCATTGTTGTATCTACCGT 58.589 36.000 0.00 0.00 0.00 4.83
2222 2672 7.557724 TCCATTTCATTGTTGTATCTACCGTA 58.442 34.615 0.00 0.00 0.00 4.02
2223 2673 8.041919 TCCATTTCATTGTTGTATCTACCGTAA 58.958 33.333 0.00 0.00 0.00 3.18
2224 2674 8.836413 CCATTTCATTGTTGTATCTACCGTAAT 58.164 33.333 0.00 0.00 0.00 1.89
2225 2675 9.864034 CATTTCATTGTTGTATCTACCGTAATC 57.136 33.333 0.00 0.00 0.00 1.75
2226 2676 9.832445 ATTTCATTGTTGTATCTACCGTAATCT 57.168 29.630 0.00 0.00 0.00 2.40
2229 2679 9.740239 TCATTGTTGTATCTACCGTAATCTAAC 57.260 33.333 0.00 0.00 0.00 2.34
2230 2680 9.745880 CATTGTTGTATCTACCGTAATCTAACT 57.254 33.333 0.00 0.00 0.00 2.24
2232 2682 9.577110 TTGTTGTATCTACCGTAATCTAACTTG 57.423 33.333 0.00 0.00 0.00 3.16
2233 2683 8.192774 TGTTGTATCTACCGTAATCTAACTTGG 58.807 37.037 0.00 0.00 0.00 3.61
2234 2684 7.281040 TGTATCTACCGTAATCTAACTTGGG 57.719 40.000 0.00 0.00 0.00 4.12
2235 2685 4.660789 TCTACCGTAATCTAACTTGGGC 57.339 45.455 0.00 0.00 0.00 5.36
2236 2686 2.704464 ACCGTAATCTAACTTGGGCC 57.296 50.000 0.00 0.00 0.00 5.80
2237 2687 1.211212 ACCGTAATCTAACTTGGGCCC 59.789 52.381 17.59 17.59 0.00 5.80
2238 2688 1.210967 CCGTAATCTAACTTGGGCCCA 59.789 52.381 24.45 24.45 0.00 5.36
2239 2689 2.356330 CCGTAATCTAACTTGGGCCCAA 60.356 50.000 34.90 34.90 0.00 4.12
2240 2690 3.551846 CGTAATCTAACTTGGGCCCAAT 58.448 45.455 37.10 25.61 35.20 3.16
2241 2691 3.315191 CGTAATCTAACTTGGGCCCAATG 59.685 47.826 37.10 29.54 35.20 2.82
2242 2692 2.459555 ATCTAACTTGGGCCCAATGG 57.540 50.000 37.10 27.69 35.20 3.16
2243 2693 1.080638 TCTAACTTGGGCCCAATGGT 58.919 50.000 37.10 28.39 35.20 3.55
2244 2694 1.005450 TCTAACTTGGGCCCAATGGTC 59.995 52.381 37.10 0.97 35.20 4.02
2250 2700 4.666105 GGCCCAATGGTCCTTCTC 57.334 61.111 0.00 0.00 0.00 2.87
2251 2701 2.002625 GGCCCAATGGTCCTTCTCT 58.997 57.895 0.00 0.00 0.00 3.10
2252 2702 0.394899 GGCCCAATGGTCCTTCTCTG 60.395 60.000 0.00 0.00 0.00 3.35
2253 2703 0.394899 GCCCAATGGTCCTTCTCTGG 60.395 60.000 0.00 0.00 0.00 3.86
2254 2704 0.995024 CCCAATGGTCCTTCTCTGGT 59.005 55.000 0.00 0.00 0.00 4.00
2255 2705 2.196595 CCCAATGGTCCTTCTCTGGTA 58.803 52.381 0.00 0.00 0.00 3.25
2256 2706 2.171448 CCCAATGGTCCTTCTCTGGTAG 59.829 54.545 0.00 0.00 0.00 3.18
2257 2707 2.420687 CCAATGGTCCTTCTCTGGTAGC 60.421 54.545 0.00 0.00 0.00 3.58
2258 2708 2.503356 CAATGGTCCTTCTCTGGTAGCT 59.497 50.000 0.00 0.00 0.00 3.32
2259 2709 1.853963 TGGTCCTTCTCTGGTAGCTC 58.146 55.000 0.00 0.00 0.00 4.09
2260 2710 1.116308 GGTCCTTCTCTGGTAGCTCC 58.884 60.000 0.00 0.00 0.00 4.70
2261 2711 1.619977 GGTCCTTCTCTGGTAGCTCCA 60.620 57.143 0.00 0.00 45.01 3.86
2269 2719 2.695561 TGGTAGCTCCAGGCATTGA 58.304 52.632 0.00 0.00 41.93 2.57
2270 2720 0.253044 TGGTAGCTCCAGGCATTGAC 59.747 55.000 0.00 0.00 41.93 3.18
2271 2721 0.464554 GGTAGCTCCAGGCATTGACC 60.465 60.000 0.00 0.00 44.79 4.02
2272 2722 0.253044 GTAGCTCCAGGCATTGACCA 59.747 55.000 0.00 0.00 44.79 4.02
2273 2723 0.543277 TAGCTCCAGGCATTGACCAG 59.457 55.000 0.00 0.00 44.79 4.00
2274 2724 1.751927 GCTCCAGGCATTGACCAGG 60.752 63.158 3.26 3.26 41.35 4.45
2275 2725 1.077212 CTCCAGGCATTGACCAGGG 60.077 63.158 8.11 5.58 37.00 4.45
2276 2726 2.043652 CCAGGCATTGACCAGGGG 60.044 66.667 0.00 0.00 32.80 4.79
2277 2727 2.615465 CCAGGCATTGACCAGGGGA 61.615 63.158 0.00 0.00 32.80 4.81
2278 2728 1.616921 CAGGCATTGACCAGGGGAT 59.383 57.895 0.00 0.00 0.00 3.85
2279 2729 0.466922 CAGGCATTGACCAGGGGATC 60.467 60.000 0.00 0.00 0.00 3.36
2280 2730 0.625683 AGGCATTGACCAGGGGATCT 60.626 55.000 0.00 0.00 0.00 2.75
2281 2731 1.140312 GGCATTGACCAGGGGATCTA 58.860 55.000 0.00 0.00 0.00 1.98
2282 2732 1.707427 GGCATTGACCAGGGGATCTAT 59.293 52.381 0.00 0.00 0.00 1.98
2283 2733 2.912956 GGCATTGACCAGGGGATCTATA 59.087 50.000 0.00 0.00 0.00 1.31
2284 2734 3.330701 GGCATTGACCAGGGGATCTATAA 59.669 47.826 0.00 0.00 0.00 0.98
2285 2735 4.018050 GGCATTGACCAGGGGATCTATAAT 60.018 45.833 0.00 0.00 0.00 1.28
2286 2736 5.517299 GGCATTGACCAGGGGATCTATAATT 60.517 44.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.875059 GCTACGGCATTGGATTAGCC 59.125 55.000 0.00 0.00 44.89 3.93
1 2 1.593196 TGCTACGGCATTGGATTAGC 58.407 50.000 0.00 0.00 44.28 3.09
16 17 1.663695 GCGAGGTAAAATGCCTGCTA 58.336 50.000 0.00 0.00 36.29 3.49
97 99 6.092748 TGTTTGAGAGCTTCAGTTTTGTTTC 58.907 36.000 0.00 0.00 37.07 2.78
145 147 5.221224 CCTTTGTTTGTTGCTCTTATGGACA 60.221 40.000 0.00 0.00 0.00 4.02
170 172 2.276827 CCATGCTTGGTGAGGAACTCG 61.277 57.143 10.48 0.00 46.85 4.18
291 295 2.542766 ATTGCTGGCGTTTACAATCG 57.457 45.000 0.00 0.00 0.00 3.34
321 325 2.224281 TGCTTCGACAGAGAAACCATGT 60.224 45.455 0.00 0.00 0.00 3.21
337 347 1.997669 ACTCGATTCTCCGTTGCTTC 58.002 50.000 0.00 0.00 0.00 3.86
345 355 6.711645 AGTACCATAGAACTACTCGATTCTCC 59.288 42.308 2.36 0.00 36.56 3.71
384 394 2.025155 GACATCGGTGAGCTTCCTCTA 58.975 52.381 0.65 0.00 38.93 2.43
395 405 1.485838 GATGCTGCTCGACATCGGTG 61.486 60.000 0.00 0.00 40.29 4.94
483 493 3.491104 CCGGGTTATCTCCTTCTTCTTCG 60.491 52.174 0.00 0.00 0.00 3.79
736 1024 1.000955 GAGAACAGAACCCTCGCAGAA 59.999 52.381 0.00 0.00 34.09 3.02
737 1025 0.603569 GAGAACAGAACCCTCGCAGA 59.396 55.000 0.00 0.00 0.00 4.26
739 1027 0.603569 GAGAGAACAGAACCCTCGCA 59.396 55.000 0.00 0.00 32.52 5.10
740 1028 0.456995 CGAGAGAACAGAACCCTCGC 60.457 60.000 0.00 0.00 39.88 5.03
764 1052 2.328589 CCTCCTCCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
784 1082 1.068121 AAAAGAGGTGGGGAGTGGAG 58.932 55.000 0.00 0.00 0.00 3.86
886 1200 3.008049 CGGGTGGGAGATTTTATAGAGGG 59.992 52.174 0.00 0.00 0.00 4.30
1010 1384 2.069430 GGGAAGAGGGGGAGCAGAG 61.069 68.421 0.00 0.00 0.00 3.35
1030 1418 3.283751 CAGTAGGATAGGGATCTAGCGG 58.716 54.545 0.00 0.00 32.98 5.52
1031 1419 3.958018 ACAGTAGGATAGGGATCTAGCG 58.042 50.000 0.00 0.00 32.98 4.26
1032 1420 4.081917 GCAACAGTAGGATAGGGATCTAGC 60.082 50.000 0.00 0.00 32.15 3.42
1036 1424 2.028930 CGGCAACAGTAGGATAGGGATC 60.029 54.545 0.00 0.00 0.00 3.36
1037 1425 1.971357 CGGCAACAGTAGGATAGGGAT 59.029 52.381 0.00 0.00 0.00 3.85
1038 1426 1.342674 ACGGCAACAGTAGGATAGGGA 60.343 52.381 0.00 0.00 0.00 4.20
1039 1427 1.120530 ACGGCAACAGTAGGATAGGG 58.879 55.000 0.00 0.00 0.00 3.53
1040 1428 1.202533 CCACGGCAACAGTAGGATAGG 60.203 57.143 0.00 0.00 0.00 2.57
1041 1429 1.480954 ACCACGGCAACAGTAGGATAG 59.519 52.381 0.00 0.00 0.00 2.08
1042 1430 1.563924 ACCACGGCAACAGTAGGATA 58.436 50.000 0.00 0.00 0.00 2.59
1043 1431 0.690762 AACCACGGCAACAGTAGGAT 59.309 50.000 0.00 0.00 0.00 3.24
1044 1432 0.034337 GAACCACGGCAACAGTAGGA 59.966 55.000 0.00 0.00 0.00 2.94
1055 1443 0.535102 AGCACCAAGAAGAACCACGG 60.535 55.000 0.00 0.00 0.00 4.94
1063 1451 1.672356 CCGGGTCAGCACCAAGAAG 60.672 63.158 0.00 0.00 45.94 2.85
1065 1453 4.329545 GCCGGGTCAGCACCAAGA 62.330 66.667 2.18 0.00 45.94 3.02
1274 1662 3.816523 CCACCTAGATCTACTTCTCGGAC 59.183 52.174 9.75 0.00 33.79 4.79
1322 1713 1.000506 TCACAGCTACTGACGGGAAAC 59.999 52.381 0.78 0.00 35.18 2.78
1324 1715 1.476891 GATCACAGCTACTGACGGGAA 59.523 52.381 0.78 0.00 35.18 3.97
1326 1717 0.103208 GGATCACAGCTACTGACGGG 59.897 60.000 0.78 0.00 35.18 5.28
1327 1718 0.248661 CGGATCACAGCTACTGACGG 60.249 60.000 0.78 0.00 35.18 4.79
1328 1719 0.452184 ACGGATCACAGCTACTGACG 59.548 55.000 0.78 0.00 35.18 4.35
1329 1720 2.531206 GAACGGATCACAGCTACTGAC 58.469 52.381 0.78 0.00 35.18 3.51
1330 1721 1.476891 GGAACGGATCACAGCTACTGA 59.523 52.381 0.78 0.00 35.18 3.41
1351 1746 6.986817 TCTTCTTACTTCTTAGCATGCATACC 59.013 38.462 21.98 0.00 0.00 2.73
1367 1762 9.482175 ACAGATACTTGATTAGGTCTTCTTACT 57.518 33.333 0.00 0.00 0.00 2.24
1399 1797 6.484288 AGATTTCCATTACCAACATCACAGA 58.516 36.000 0.00 0.00 0.00 3.41
1463 1863 6.409704 GCCACAAGCAGGATAATATGAGATA 58.590 40.000 0.00 0.00 42.97 1.98
1464 1864 5.251764 GCCACAAGCAGGATAATATGAGAT 58.748 41.667 0.00 0.00 42.97 2.75
1465 1865 4.645535 GCCACAAGCAGGATAATATGAGA 58.354 43.478 0.00 0.00 42.97 3.27
1490 1890 8.562892 CAGACCATATAAAATAACAGAAGCAGG 58.437 37.037 0.00 0.00 0.00 4.85
1538 1938 5.661056 TCCAACCACTAATCAGTACTCTG 57.339 43.478 0.00 0.00 42.54 3.35
1539 1939 5.336531 CGTTCCAACCACTAATCAGTACTCT 60.337 44.000 0.00 0.00 32.21 3.24
1540 1940 4.863131 CGTTCCAACCACTAATCAGTACTC 59.137 45.833 0.00 0.00 32.21 2.59
1541 1941 4.525487 TCGTTCCAACCACTAATCAGTACT 59.475 41.667 0.00 0.00 32.21 2.73
1542 1942 4.813027 TCGTTCCAACCACTAATCAGTAC 58.187 43.478 0.00 0.00 32.21 2.73
1543 1943 5.471556 TTCGTTCCAACCACTAATCAGTA 57.528 39.130 0.00 0.00 32.21 2.74
1544 1944 4.345859 TTCGTTCCAACCACTAATCAGT 57.654 40.909 0.00 0.00 34.42 3.41
1545 1945 4.332819 GGATTCGTTCCAACCACTAATCAG 59.667 45.833 2.81 0.00 44.74 2.90
1558 1958 4.271291 GTCATTCAGCTAAGGATTCGTTCC 59.729 45.833 0.00 0.00 45.85 3.62
1578 1978 2.236146 CTGGTACACTATTGCTGGGTCA 59.764 50.000 0.00 0.00 0.00 4.02
1581 1981 1.668419 GCTGGTACACTATTGCTGGG 58.332 55.000 0.00 0.00 0.00 4.45
1609 2009 0.961019 GCATCAGCAACAAGACCCAA 59.039 50.000 0.00 0.00 41.58 4.12
1611 2011 1.251251 AAGCATCAGCAACAAGACCC 58.749 50.000 0.00 0.00 45.49 4.46
1636 2036 7.511959 AGGAAGTACAGAAGTTTTCAAATCC 57.488 36.000 0.00 0.00 0.00 3.01
1713 2113 7.428020 TGTTGAGCTTGAATATTTGCATATCC 58.572 34.615 10.25 0.00 0.00 2.59
1717 2117 6.327934 GTCTGTTGAGCTTGAATATTTGCAT 58.672 36.000 10.25 0.00 0.00 3.96
1791 2191 0.687354 AAGTGATGGCTCGGTTCAGT 59.313 50.000 0.00 0.00 0.00 3.41
1869 2279 1.462791 CTCGGAAAAACACGCACAAC 58.537 50.000 0.00 0.00 0.00 3.32
1885 2295 2.507992 CACGGCAGAGAAGGCTCG 60.508 66.667 0.00 0.00 45.98 5.03
1914 2324 6.306596 GGAAACAATCAATCGAAAAAGAGAGC 59.693 38.462 0.00 0.00 0.00 4.09
1919 2329 8.970691 ATACTGGAAACAATCAATCGAAAAAG 57.029 30.769 0.00 0.00 42.06 2.27
1925 2335 5.586243 ACCTGATACTGGAAACAATCAATCG 59.414 40.000 0.00 0.00 37.19 3.34
1934 2355 5.123979 GGTTTCATCACCTGATACTGGAAAC 59.876 44.000 14.69 14.69 39.91 2.78
2043 2464 0.727122 GCAATGAGCACAACGTGAGC 60.727 55.000 0.00 0.00 44.79 4.26
2097 2535 9.667989 AAGCTGCATAAAATTTCAATTGAAAAC 57.332 25.926 31.39 17.26 45.81 2.43
2102 2540 8.714179 TCAGAAAGCTGCATAAAATTTCAATTG 58.286 29.630 1.02 0.00 42.01 2.32
2104 2542 8.475331 CTCAGAAAGCTGCATAAAATTTCAAT 57.525 30.769 1.02 0.00 42.01 2.57
2126 2564 8.770438 AAATGTTTAAACTGACAAAAAGCTCA 57.230 26.923 18.72 0.00 0.00 4.26
2157 2595 4.142049 GACCAACAAAAGTCAAATGGGACA 60.142 41.667 0.00 0.00 40.29 4.02
2160 2598 4.141959 ACAGACCAACAAAAGTCAAATGGG 60.142 41.667 0.00 0.00 35.38 4.00
2161 2599 5.009854 ACAGACCAACAAAAGTCAAATGG 57.990 39.130 0.00 0.00 35.38 3.16
2176 2626 3.945285 GAGTTTCCAACAAAGACAGACCA 59.055 43.478 0.00 0.00 0.00 4.02
2194 2644 7.065803 CGGTAGATACAACAATGAAATGGAGTT 59.934 37.037 0.00 0.00 0.00 3.01
2197 2647 6.411376 ACGGTAGATACAACAATGAAATGGA 58.589 36.000 0.00 0.00 0.00 3.41
2209 2659 7.685155 GCCCAAGTTAGATTACGGTAGATACAA 60.685 40.741 0.00 0.00 0.00 2.41
2211 2661 6.155136 GCCCAAGTTAGATTACGGTAGATAC 58.845 44.000 0.00 0.00 0.00 2.24
2215 2665 3.493873 GGGCCCAAGTTAGATTACGGTAG 60.494 52.174 19.95 0.00 0.00 3.18
2216 2666 2.435437 GGGCCCAAGTTAGATTACGGTA 59.565 50.000 19.95 0.00 0.00 4.02
2217 2667 1.211212 GGGCCCAAGTTAGATTACGGT 59.789 52.381 19.95 0.00 0.00 4.83
2218 2668 1.210967 TGGGCCCAAGTTAGATTACGG 59.789 52.381 26.33 0.00 0.00 4.02
2219 2669 2.702592 TGGGCCCAAGTTAGATTACG 57.297 50.000 26.33 0.00 0.00 3.18
2220 2670 3.636764 CCATTGGGCCCAAGTTAGATTAC 59.363 47.826 38.82 1.18 39.47 1.89
2221 2671 3.270960 ACCATTGGGCCCAAGTTAGATTA 59.729 43.478 38.82 16.53 39.47 1.75
2222 2672 2.044353 ACCATTGGGCCCAAGTTAGATT 59.956 45.455 38.82 20.37 39.47 2.40
2223 2673 1.645919 ACCATTGGGCCCAAGTTAGAT 59.354 47.619 38.82 21.14 39.47 1.98
2224 2674 1.005450 GACCATTGGGCCCAAGTTAGA 59.995 52.381 38.82 18.94 39.47 2.10
2225 2675 1.474330 GACCATTGGGCCCAAGTTAG 58.526 55.000 38.82 27.95 39.47 2.34
2226 2676 3.681909 GACCATTGGGCCCAAGTTA 57.318 52.632 38.82 20.17 39.47 2.24
2227 2677 4.539235 GACCATTGGGCCCAAGTT 57.461 55.556 38.82 26.18 39.47 2.66
2234 2684 0.394899 CCAGAGAAGGACCATTGGGC 60.395 60.000 7.78 3.14 37.90 5.36
2235 2685 0.995024 ACCAGAGAAGGACCATTGGG 59.005 55.000 7.78 0.00 41.29 4.12
2236 2686 2.420687 GCTACCAGAGAAGGACCATTGG 60.421 54.545 0.00 0.00 0.00 3.16
2237 2687 2.503356 AGCTACCAGAGAAGGACCATTG 59.497 50.000 0.00 0.00 0.00 2.82
2238 2688 2.769095 GAGCTACCAGAGAAGGACCATT 59.231 50.000 0.00 0.00 0.00 3.16
2239 2689 2.393646 GAGCTACCAGAGAAGGACCAT 58.606 52.381 0.00 0.00 0.00 3.55
2240 2690 1.619977 GGAGCTACCAGAGAAGGACCA 60.620 57.143 0.00 0.00 38.79 4.02
2241 2691 1.116308 GGAGCTACCAGAGAAGGACC 58.884 60.000 0.00 0.00 38.79 4.46
2242 2692 1.853963 TGGAGCTACCAGAGAAGGAC 58.146 55.000 0.00 0.00 44.64 3.85
2252 2702 0.464554 GGTCAATGCCTGGAGCTACC 60.465 60.000 0.00 0.00 44.23 3.18
2253 2703 0.253044 TGGTCAATGCCTGGAGCTAC 59.747 55.000 0.00 0.00 44.23 3.58
2254 2704 0.543277 CTGGTCAATGCCTGGAGCTA 59.457 55.000 0.00 0.00 44.23 3.32
2255 2705 1.302285 CTGGTCAATGCCTGGAGCT 59.698 57.895 0.00 0.00 44.23 4.09
2256 2706 1.751927 CCTGGTCAATGCCTGGAGC 60.752 63.158 11.96 0.00 46.74 4.70
2257 2707 1.077212 CCCTGGTCAATGCCTGGAG 60.077 63.158 16.69 7.17 46.74 3.86
2258 2708 2.615465 CCCCTGGTCAATGCCTGGA 61.615 63.158 16.69 0.00 46.74 3.86
2259 2709 1.941403 ATCCCCTGGTCAATGCCTGG 61.941 60.000 10.88 10.88 44.38 4.45
2260 2710 0.466922 GATCCCCTGGTCAATGCCTG 60.467 60.000 0.00 0.00 0.00 4.85
2261 2711 0.625683 AGATCCCCTGGTCAATGCCT 60.626 55.000 0.00 0.00 0.00 4.75
2262 2712 1.140312 TAGATCCCCTGGTCAATGCC 58.860 55.000 0.00 0.00 0.00 4.40
2263 2713 4.640771 TTATAGATCCCCTGGTCAATGC 57.359 45.455 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.