Multiple sequence alignment - TraesCS6D01G401300

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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 TraesCS6D01G401300 chr6D 100.000 2633 0 0 1 2633 470615469 470612837 0.000000e+00 4863
1 TraesCS6D01G401300 chr6D 97.000 200 2 1 2438 2633 470607822 470607623 1.510000e-87 333
2 TraesCS6D01G401300 chr6B 93.543 1301 38 26 648 1922 720528254 720529534 0.000000e+00 1895
3 TraesCS6D01G401300 chr6B 91.339 635 45 7 17 648 720520918 720521545 0.000000e+00 859
4 TraesCS6D01G401300 chr6B 93.571 140 6 2 2383 2519 720555785 720555924 3.440000e-49 206
5 TraesCS6D01G401300 chr6A 94.371 835 38 4 1095 1925 615439517 615438688 0.000000e+00 1273
6 TraesCS6D01G401300 chr6A 90.174 631 47 9 20 648 615441801 615441184 0.000000e+00 808
7 TraesCS6D01G401300 chr6A 91.783 572 21 10 2084 2633 615438689 615438122 0.000000e+00 773
8 TraesCS6D01G401300 chr6A 96.171 444 13 2 648 1088 615439924 615439482 0.000000e+00 723
9 TraesCS6D01G401300 chr6A 78.187 353 51 19 20 350 184860032 184860380 4.440000e-48 202
10 TraesCS6D01G401300 chr3D 93.567 171 10 1 1915 2084 526507079 526506909 1.210000e-63 254
11 TraesCS6D01G401300 chr3D 94.012 167 9 1 1923 2088 59924379 59924213 4.350000e-63 252
12 TraesCS6D01G401300 chr3D 74.640 347 68 13 23 350 174525771 174525426 4.570000e-28 135
13 TraesCS6D01G401300 chr1D 94.012 167 9 1 1924 2089 311986774 311986608 4.350000e-63 252
14 TraesCS6D01G401300 chr1D 80.588 340 52 12 20 350 420268105 420268439 1.560000e-62 250
15 TraesCS6D01G401300 chr7A 91.908 173 12 2 1924 2094 83737378 83737206 9.420000e-60 241
16 TraesCS6D01G401300 chr5D 92.353 170 11 2 1921 2088 60140931 60140762 9.420000e-60 241
17 TraesCS6D01G401300 chr5D 77.904 353 52 18 20 350 194591712 194591364 2.070000e-46 196
18 TraesCS6D01G401300 chr7D 91.061 179 13 3 1909 2085 171307974 171308151 3.390000e-59 239
19 TraesCS6D01G401300 chr2D 91.379 174 13 2 1917 2088 37065266 37065439 1.220000e-58 237
20 TraesCS6D01G401300 chr2D 90.110 182 15 2 1914 2092 83920424 83920605 1.580000e-57 233
21 TraesCS6D01G401300 chr3B 92.638 163 12 0 1924 2086 54755073 54754911 4.380000e-58 235
22 TraesCS6D01G401300 chr4A 78.393 361 52 17 12 350 630533584 630533940 7.380000e-51 211
23 TraesCS6D01G401300 chr4A 78.063 351 56 15 20 351 512660633 512660981 4.440000e-48 202
24 TraesCS6D01G401300 chr4A 76.633 398 62 23 17 391 666340665 666341054 9.620000e-45 191
25 TraesCS6D01G401300 chr4A 76.633 398 62 23 17 391 666403564 666403953 9.620000e-45 191


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 TraesCS6D01G401300 chr6D 470612837 470615469 2632 True 4863.00 4863 100.00000 1 2633 1 chr6D.!!$R2 2632
1 TraesCS6D01G401300 chr6B 720528254 720529534 1280 False 1895.00 1895 93.54300 648 1922 1 chr6B.!!$F2 1274
2 TraesCS6D01G401300 chr6B 720520918 720521545 627 False 859.00 859 91.33900 17 648 1 chr6B.!!$F1 631
3 TraesCS6D01G401300 chr6A 615438122 615441801 3679 True 894.25 1273 93.12475 20 2633 4 chr6A.!!$R1 2613

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
350 354 0.394192 TGTGCAGTTCTGTCTCCAGG 59.606 55.0 0.0 0.0 39.31 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 3640 1.645402 TAGCTGGGGAATCCAAGGCC 61.645 60.0 0.09 0.0 46.51 5.19 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
18 19 2.682893 CTGAACGGCCATCAGTAGC 58.317 57.895 21.87 1.96 39.54 3.58
27 28 3.702792 GGCCATCAGTAGCTATCTAGGA 58.297 50.000 0.00 0.00 0.00 2.94
31 32 5.329399 CCATCAGTAGCTATCTAGGAACCT 58.671 45.833 0.00 0.00 0.00 3.50
35 36 6.065374 TCAGTAGCTATCTAGGAACCTCAAG 58.935 44.000 0.00 0.00 0.00 3.02
45 46 2.091333 AGGAACCTCAAGCCTTGGAAAA 60.091 45.455 4.30 0.00 0.00 2.29
53 54 6.723977 ACCTCAAGCCTTGGAAAAATAACATA 59.276 34.615 4.30 0.00 0.00 2.29
60 61 9.599866 AGCCTTGGAAAAATAACATATTTAAGC 57.400 29.630 0.00 0.00 0.00 3.09
97 99 5.116180 TCTATGATCAACGCCTTTAGTTGG 58.884 41.667 0.00 0.00 46.36 3.77
111 113 8.290325 CGCCTTTAGTTGGAATAATTTCTATCC 58.710 37.037 0.00 0.00 32.16 2.59
160 162 5.982890 AAAATAGAAATGTGACCCTGTGG 57.017 39.130 0.00 0.00 37.80 4.17
204 206 5.186797 AGTCAAAACCTCATGTCCAAACAAA 59.813 36.000 0.00 0.00 39.30 2.83
207 209 3.733443 ACCTCATGTCCAAACAAAAGC 57.267 42.857 0.00 0.00 39.30 3.51
287 290 7.970384 TCACAAGACAATATAAACTTAAGGCG 58.030 34.615 7.53 0.00 0.00 5.52
350 354 0.394192 TGTGCAGTTCTGTCTCCAGG 59.606 55.000 0.00 0.00 39.31 4.45
351 355 0.952984 GTGCAGTTCTGTCTCCAGGC 60.953 60.000 0.00 0.00 39.31 4.85
352 356 1.123861 TGCAGTTCTGTCTCCAGGCT 61.124 55.000 1.78 0.00 39.31 4.58
386 390 3.116590 TCATCCCTATGGACTGGAGTGAT 60.117 47.826 0.00 0.00 45.58 3.06
392 396 4.022762 CCTATGGACTGGAGTGATACTTCG 60.023 50.000 0.00 0.00 0.00 3.79
476 480 3.278574 TGCCTATGCCAGTTAACATGAC 58.721 45.455 8.61 0.00 36.33 3.06
539 544 4.412528 ACCCATATCTCCTTGTCCTAAACC 59.587 45.833 0.00 0.00 0.00 3.27
664 1929 1.783711 GCATACGCTTGATCACTCGAG 59.216 52.381 19.01 11.84 36.16 4.04
683 1948 6.070710 ACTCGAGGGCTAAGATTAAAAGTTCT 60.071 38.462 18.41 0.00 0.00 3.01
688 1953 9.668497 GAGGGCTAAGATTAAAAGTTCTTCTTA 57.332 33.333 0.00 0.00 35.02 2.10
1096 2370 4.609018 CCCCCATAGCGCTCGGTG 62.609 72.222 16.34 11.99 0.00 4.94
1105 2379 3.147595 CGCTCGGTGATCTGGGGA 61.148 66.667 0.00 0.00 0.00 4.81
1106 2380 2.501610 GCTCGGTGATCTGGGGAC 59.498 66.667 0.00 0.00 0.00 4.46
1107 2381 2.808315 CTCGGTGATCTGGGGACG 59.192 66.667 0.00 0.00 0.00 4.79
1108 2382 2.758327 TCGGTGATCTGGGGACGG 60.758 66.667 0.00 0.00 38.41 4.79
1109 2383 4.530857 CGGTGATCTGGGGACGGC 62.531 72.222 0.00 0.00 36.33 5.68
1110 2384 4.530857 GGTGATCTGGGGACGGCG 62.531 72.222 4.80 4.80 36.33 6.46
1111 2385 4.530857 GTGATCTGGGGACGGCGG 62.531 72.222 13.24 0.00 36.33 6.13
1129 2403 3.646715 TGGAGACCGCCCCCAAAG 61.647 66.667 0.00 0.00 0.00 2.77
1170 2444 0.456221 TCAAAAGGTTTTGCGCCGAA 59.544 45.000 4.18 0.00 45.35 4.30
1211 2485 2.725815 CGACATGATCGCGCGCTA 60.726 61.111 30.48 20.37 45.52 4.26
1212 2486 2.840016 GACATGATCGCGCGCTAC 59.160 61.111 30.48 19.44 0.00 3.58
1298 2572 1.000145 CTCCTTCTTAAAGCGTCCGC 59.000 55.000 2.94 2.94 42.33 5.54
1605 2879 2.599597 GCCATGGCTGTCCTGGAT 59.400 61.111 29.98 0.00 38.26 3.41
1614 2888 0.036952 CTGTCCTGGATGTGCTCGTT 60.037 55.000 0.00 0.00 0.00 3.85
1645 2919 9.719355 AAGTGACCAAATAAAGAAAAACAAACT 57.281 25.926 0.00 0.00 0.00 2.66
1657 2935 8.579682 AAGAAAAACAAACTCTCATTGCATAC 57.420 30.769 0.00 0.00 0.00 2.39
1658 2936 7.945134 AGAAAAACAAACTCTCATTGCATACT 58.055 30.769 0.00 0.00 0.00 2.12
1659 2937 9.066892 AGAAAAACAAACTCTCATTGCATACTA 57.933 29.630 0.00 0.00 0.00 1.82
1660 2938 9.118236 GAAAAACAAACTCTCATTGCATACTAC 57.882 33.333 0.00 0.00 0.00 2.73
1661 2939 7.986085 AAACAAACTCTCATTGCATACTACT 57.014 32.000 0.00 0.00 0.00 2.57
1662 2940 9.502091 AAAACAAACTCTCATTGCATACTACTA 57.498 29.630 0.00 0.00 0.00 1.82
1702 2987 9.581099 GTTGTTTGATTTTTAGTTTCCTTGAGA 57.419 29.630 0.00 0.00 0.00 3.27
1722 3007 6.920817 TGAGAATATATGTACGGTCATGGTC 58.079 40.000 0.00 0.00 0.00 4.02
1935 3227 9.518906 TTTTTGTTTTTAAATACTCCCTCGTTC 57.481 29.630 9.70 0.00 0.00 3.95
1936 3228 6.806388 TGTTTTTAAATACTCCCTCGTTCC 57.194 37.500 9.70 0.00 0.00 3.62
1937 3229 6.536447 TGTTTTTAAATACTCCCTCGTTCCT 58.464 36.000 9.70 0.00 0.00 3.36
1938 3230 7.678837 TGTTTTTAAATACTCCCTCGTTCCTA 58.321 34.615 9.70 0.00 0.00 2.94
1939 3231 8.156165 TGTTTTTAAATACTCCCTCGTTCCTAA 58.844 33.333 9.70 0.00 0.00 2.69
1940 3232 9.002600 GTTTTTAAATACTCCCTCGTTCCTAAA 57.997 33.333 1.96 0.00 0.00 1.85
1941 3233 9.743581 TTTTTAAATACTCCCTCGTTCCTAAAT 57.256 29.630 0.00 0.00 0.00 1.40
1949 3241 8.493787 ACTCCCTCGTTCCTAAATATAAATCT 57.506 34.615 0.00 0.00 0.00 2.40
1950 3242 8.935741 ACTCCCTCGTTCCTAAATATAAATCTT 58.064 33.333 0.00 0.00 0.00 2.40
1951 3243 9.780186 CTCCCTCGTTCCTAAATATAAATCTTT 57.220 33.333 0.00 0.00 0.00 2.52
1952 3244 9.555727 TCCCTCGTTCCTAAATATAAATCTTTG 57.444 33.333 0.00 0.00 0.00 2.77
1953 3245 9.338622 CCCTCGTTCCTAAATATAAATCTTTGT 57.661 33.333 0.00 0.00 0.00 2.83
1969 3261 7.741554 AATCTTTGTAGAGATTCCACTAGGT 57.258 36.000 0.00 0.00 41.33 3.08
1970 3262 6.531503 TCTTTGTAGAGATTCCACTAGGTG 57.468 41.667 0.00 0.00 35.89 4.00
1971 3263 6.098982 ATCTTTGTAGAGATTCCACTAGGTGG 59.901 42.308 10.16 10.16 43.42 4.61
1972 3264 8.026963 ATCTTTGTAGAGATTCCACTAGGTGGA 61.027 40.741 14.51 14.51 46.19 4.02
1984 3276 5.171147 CACTAGGTGGACTACATACGAAG 57.829 47.826 0.00 0.00 0.00 3.79
1985 3277 3.631227 ACTAGGTGGACTACATACGAAGC 59.369 47.826 0.00 0.00 0.00 3.86
1986 3278 2.453521 AGGTGGACTACATACGAAGCA 58.546 47.619 0.00 0.00 0.00 3.91
1987 3279 2.829720 AGGTGGACTACATACGAAGCAA 59.170 45.455 0.00 0.00 0.00 3.91
1988 3280 3.259876 AGGTGGACTACATACGAAGCAAA 59.740 43.478 0.00 0.00 0.00 3.68
1989 3281 3.998341 GGTGGACTACATACGAAGCAAAA 59.002 43.478 0.00 0.00 0.00 2.44
1990 3282 4.634443 GGTGGACTACATACGAAGCAAAAT 59.366 41.667 0.00 0.00 0.00 1.82
1991 3283 5.447279 GGTGGACTACATACGAAGCAAAATG 60.447 44.000 0.00 0.00 0.00 2.32
1992 3284 5.350365 GTGGACTACATACGAAGCAAAATGA 59.650 40.000 0.00 0.00 0.00 2.57
1993 3285 5.935206 TGGACTACATACGAAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
1994 3286 6.597672 TGGACTACATACGAAGCAAAATGAAT 59.402 34.615 0.00 0.00 0.00 2.57
1995 3287 6.907212 GGACTACATACGAAGCAAAATGAATG 59.093 38.462 0.00 0.00 0.00 2.67
1996 3288 7.201609 GGACTACATACGAAGCAAAATGAATGA 60.202 37.037 0.00 0.00 0.00 2.57
1997 3289 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
1998 3290 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
1999 3291 7.975866 ACATACGAAGCAAAATGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
2000 3292 7.765307 ACATACGAAGCAAAATGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
2001 3293 8.892723 ACATACGAAGCAAAATGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
2002 3294 9.162793 CATACGAAGCAAAATGAATGAATCTAC 57.837 33.333 0.00 0.00 0.00 2.59
2003 3295 7.144722 ACGAAGCAAAATGAATGAATCTACA 57.855 32.000 0.00 0.00 0.00 2.74
2004 3296 7.023575 ACGAAGCAAAATGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
2005 3297 7.094634 ACGAAGCAAAATGAATGAATCTACACT 60.095 33.333 0.00 0.00 0.00 3.55
2006 3298 7.752239 CGAAGCAAAATGAATGAATCTACACTT 59.248 33.333 0.00 0.00 0.00 3.16
2019 3311 8.565896 TGAATCTACACTTAAAATGCATCTGT 57.434 30.769 0.00 0.00 0.00 3.41
2020 3312 9.665719 TGAATCTACACTTAAAATGCATCTGTA 57.334 29.630 0.00 0.00 0.00 2.74
2027 3319 8.840321 ACACTTAAAATGCATCTGTATACATCC 58.160 33.333 5.91 0.00 0.00 3.51
2028 3320 8.011673 CACTTAAAATGCATCTGTATACATCCG 58.988 37.037 5.91 0.00 0.00 4.18
2029 3321 7.715249 ACTTAAAATGCATCTGTATACATCCGT 59.285 33.333 5.91 0.00 0.00 4.69
2030 3322 9.203421 CTTAAAATGCATCTGTATACATCCGTA 57.797 33.333 5.91 0.00 0.00 4.02
2031 3323 9.719355 TTAAAATGCATCTGTATACATCCGTAT 57.281 29.630 5.91 0.18 41.34 3.06
2032 3324 7.601073 AAATGCATCTGTATACATCCGTATG 57.399 36.000 5.91 6.91 38.79 2.39
2034 3326 5.469479 TGCATCTGTATACATCCGTATGTG 58.531 41.667 5.91 0.00 45.99 3.21
2035 3327 4.864806 GCATCTGTATACATCCGTATGTGG 59.135 45.833 5.91 0.00 45.99 4.17
2036 3328 5.566826 GCATCTGTATACATCCGTATGTGGT 60.567 44.000 5.91 0.00 45.99 4.16
2037 3329 6.455647 CATCTGTATACATCCGTATGTGGTT 58.544 40.000 5.91 0.00 45.99 3.67
2038 3330 6.080648 TCTGTATACATCCGTATGTGGTTC 57.919 41.667 5.91 0.00 45.99 3.62
2039 3331 5.595133 TCTGTATACATCCGTATGTGGTTCA 59.405 40.000 5.91 0.00 45.99 3.18
2040 3332 6.266786 TCTGTATACATCCGTATGTGGTTCAT 59.733 38.462 5.91 0.00 45.99 2.57
2041 3333 7.449086 TCTGTATACATCCGTATGTGGTTCATA 59.551 37.037 5.91 0.00 45.99 2.15
2042 3334 7.599171 TGTATACATCCGTATGTGGTTCATAG 58.401 38.462 3.56 0.00 45.99 2.23
2043 3335 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
2044 3336 7.770366 ATACATCCGTATGTGGTTCATAGTA 57.230 36.000 3.56 0.00 45.99 1.82
2045 3337 6.085555 ACATCCGTATGTGGTTCATAGTAG 57.914 41.667 0.00 0.00 44.79 2.57
2046 3338 5.831525 ACATCCGTATGTGGTTCATAGTAGA 59.168 40.000 0.00 0.00 44.79 2.59
2047 3339 6.493802 ACATCCGTATGTGGTTCATAGTAGAT 59.506 38.462 0.00 0.00 44.79 1.98
2048 3340 6.971726 TCCGTATGTGGTTCATAGTAGATT 57.028 37.500 0.00 0.00 39.36 2.40
2049 3341 6.978338 TCCGTATGTGGTTCATAGTAGATTC 58.022 40.000 0.00 0.00 39.36 2.52
2050 3342 6.776116 TCCGTATGTGGTTCATAGTAGATTCT 59.224 38.462 0.00 0.00 39.36 2.40
2051 3343 7.040617 TCCGTATGTGGTTCATAGTAGATTCTC 60.041 40.741 0.00 0.00 39.36 2.87
2052 3344 7.040340 CCGTATGTGGTTCATAGTAGATTCTCT 60.040 40.741 0.00 0.00 39.36 3.10
2053 3345 9.000486 CGTATGTGGTTCATAGTAGATTCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
2082 3374 9.819267 AAGACTTATATTTAGAAACGGAAGGAG 57.181 33.333 0.00 0.00 0.00 3.69
2083 3375 8.979534 AGACTTATATTTAGAAACGGAAGGAGT 58.020 33.333 0.00 0.00 0.00 3.85
2137 3430 7.075741 GGTATGCGTATGATTCAACCAAATAC 58.924 38.462 0.00 0.00 0.00 1.89
2298 3606 5.397142 AGGATTGCAAAGAGAAAACCATC 57.603 39.130 1.71 0.00 0.00 3.51
2304 3612 4.588106 TGCAAAGAGAAAACCATCCAATGA 59.412 37.500 0.00 0.00 0.00 2.57
2332 3640 2.752354 TGGCATTTGGAAACCTATGACG 59.248 45.455 0.00 0.00 30.59 4.35
2359 3670 3.527253 TGGATTCCCCAGCTATTTTCTGA 59.473 43.478 0.00 0.00 40.82 3.27
2400 3711 5.804639 ACTAGTTTTACATGCATGGACTGA 58.195 37.500 29.41 4.50 0.00 3.41
2428 3739 3.555966 ACAAGTTTCCCTCTGTCAAAGG 58.444 45.455 0.00 0.00 0.00 3.11
2435 3746 1.608283 CCCTCTGTCAAAGGTTCGGTC 60.608 57.143 0.00 0.00 31.51 4.79
2444 3755 2.109425 AAGGTTCGGTCCATACTTGC 57.891 50.000 0.00 0.00 0.00 4.01
2462 3773 1.210931 CGCCACATGTTCAAGGCTG 59.789 57.895 19.40 11.18 44.85 4.85
2511 3825 3.877508 AGACAAAAACTAGTGCCACTCAC 59.122 43.478 0.00 0.00 45.98 3.51
2540 3854 0.316204 GCTTATAAGGGCCGAGCGTA 59.684 55.000 14.28 0.00 0.00 4.42
2560 3874 5.995897 GCGTACCCTAGGTCATTAATTTGAT 59.004 40.000 8.29 0.00 37.09 2.57
2563 3877 7.713507 CGTACCCTAGGTCATTAATTTGATCAA 59.286 37.037 8.29 3.38 37.09 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.176680 AGCTACTGATGGCCGTTCAG 59.823 55.000 26.00 26.00 44.95 3.02
1 2 1.480789 TAGCTACTGATGGCCGTTCA 58.519 50.000 0.00 3.10 31.21 3.18
2 3 2.297597 AGATAGCTACTGATGGCCGTTC 59.702 50.000 0.00 0.00 31.21 3.95
3 4 2.320781 AGATAGCTACTGATGGCCGTT 58.679 47.619 0.00 0.00 31.21 4.44
4 5 2.002505 AGATAGCTACTGATGGCCGT 57.997 50.000 0.00 0.00 31.21 5.68
5 6 2.425312 CCTAGATAGCTACTGATGGCCG 59.575 54.545 0.00 0.00 31.21 6.13
6 7 3.702792 TCCTAGATAGCTACTGATGGCC 58.297 50.000 0.00 0.00 31.21 5.36
7 8 4.081917 GGTTCCTAGATAGCTACTGATGGC 60.082 50.000 0.00 0.00 0.00 4.40
8 9 5.329399 AGGTTCCTAGATAGCTACTGATGG 58.671 45.833 0.00 0.00 0.00 3.51
9 10 6.007076 TGAGGTTCCTAGATAGCTACTGATG 58.993 44.000 0.00 0.00 0.00 3.07
10 11 6.207509 TGAGGTTCCTAGATAGCTACTGAT 57.792 41.667 0.00 0.00 0.00 2.90
11 12 5.648330 TGAGGTTCCTAGATAGCTACTGA 57.352 43.478 0.00 0.00 0.00 3.41
12 13 5.278758 GCTTGAGGTTCCTAGATAGCTACTG 60.279 48.000 0.00 0.00 0.00 2.74
13 14 4.830600 GCTTGAGGTTCCTAGATAGCTACT 59.169 45.833 0.00 0.00 0.00 2.57
14 15 4.021807 GGCTTGAGGTTCCTAGATAGCTAC 60.022 50.000 0.00 0.00 0.00 3.58
15 16 4.140900 AGGCTTGAGGTTCCTAGATAGCTA 60.141 45.833 0.00 0.00 0.00 3.32
16 17 2.969262 GGCTTGAGGTTCCTAGATAGCT 59.031 50.000 0.00 0.00 0.00 3.32
17 18 2.969262 AGGCTTGAGGTTCCTAGATAGC 59.031 50.000 0.00 0.00 0.00 2.97
18 19 4.202305 CCAAGGCTTGAGGTTCCTAGATAG 60.202 50.000 28.18 2.50 0.00 2.08
27 28 5.365314 TGTTATTTTTCCAAGGCTTGAGGTT 59.635 36.000 28.18 10.09 0.00 3.50
35 36 9.377312 TGCTTAAATATGTTATTTTTCCAAGGC 57.623 29.630 0.00 0.00 0.00 4.35
70 71 7.865706 ACTAAAGGCGTTGATCATAGATTTT 57.134 32.000 0.00 0.00 0.00 1.82
86 88 9.131791 TGGATAGAAATTATTCCAACTAAAGGC 57.868 33.333 0.00 0.00 36.12 4.35
136 138 7.410174 TCCACAGGGTCACATTTCTATTTTAT 58.590 34.615 0.00 0.00 34.93 1.40
151 153 2.158667 TCTTTTCCAACTCCACAGGGTC 60.159 50.000 0.00 0.00 34.93 4.46
249 252 9.850628 ATATTGTCTTGTGATGAATGTCAAAAG 57.149 29.630 1.30 1.30 42.37 2.27
266 269 7.336396 AGGACGCCTTAAGTTTATATTGTCTT 58.664 34.615 0.97 0.00 0.00 3.01
283 286 2.028020 CCTACTCTTTTCAAGGACGCCT 60.028 50.000 0.00 0.00 33.87 5.52
287 290 3.418684 TGGCCTACTCTTTTCAAGGAC 57.581 47.619 3.32 0.00 37.68 3.85
350 354 1.099879 GGATGACACCATGCTGGAGC 61.100 60.000 8.91 0.00 40.96 4.70
351 355 0.465097 GGGATGACACCATGCTGGAG 60.465 60.000 8.91 4.08 40.96 3.86
352 356 0.915872 AGGGATGACACCATGCTGGA 60.916 55.000 8.91 0.00 40.96 3.86
370 374 4.557695 GCGAAGTATCACTCCAGTCCATAG 60.558 50.000 0.00 0.00 0.00 2.23
372 376 2.101582 GCGAAGTATCACTCCAGTCCAT 59.898 50.000 0.00 0.00 0.00 3.41
386 390 4.214971 GGAGTATCGTATCTTGGCGAAGTA 59.785 45.833 8.41 0.00 40.61 2.24
392 396 5.593010 GGATATGGAGTATCGTATCTTGGC 58.407 45.833 0.00 0.00 40.15 4.52
476 480 7.439157 ACATGATATATGTGGGATGTTTTCG 57.561 36.000 0.00 0.00 0.00 3.46
508 513 7.517604 AGGACAAGGAGATATGGGTGTTATATT 59.482 37.037 0.00 0.00 0.00 1.28
509 514 7.025620 AGGACAAGGAGATATGGGTGTTATAT 58.974 38.462 0.00 0.00 0.00 0.86
515 520 5.368989 GTTTAGGACAAGGAGATATGGGTG 58.631 45.833 0.00 0.00 0.00 4.61
664 1929 8.675504 GGTAAGAAGAACTTTTAATCTTAGCCC 58.324 37.037 10.38 0.32 41.63 5.19
926 2192 9.768662 CAGTCCATATATATAAGCACATGCATA 57.231 33.333 6.64 0.00 45.16 3.14
1096 2370 4.530857 CACCGCCGTCCCCAGATC 62.531 72.222 0.00 0.00 0.00 2.75
1111 2385 3.920093 CTTTGGGGGCGGTCTCCAC 62.920 68.421 0.00 0.00 0.00 4.02
1112 2386 3.646715 CTTTGGGGGCGGTCTCCA 61.647 66.667 0.00 0.00 0.00 3.86
1211 2485 1.660575 CCTTTGCACTCGTCGTCGT 60.661 57.895 1.33 0.00 38.33 4.34
1212 2486 3.000080 GCCTTTGCACTCGTCGTCG 62.000 63.158 0.00 0.00 37.47 5.12
1213 2487 2.853914 GCCTTTGCACTCGTCGTC 59.146 61.111 0.00 0.00 37.47 4.20
1605 2879 2.610374 GGTCACTTTGTTAACGAGCACA 59.390 45.455 0.26 0.00 0.00 4.57
1645 2919 6.968263 AGAGCTTAGTAGTATGCAATGAGA 57.032 37.500 15.61 0.00 32.82 3.27
1657 2935 9.651718 CAAACAACTTTAACAAGAGCTTAGTAG 57.348 33.333 0.00 0.00 33.72 2.57
1658 2936 9.386010 TCAAACAACTTTAACAAGAGCTTAGTA 57.614 29.630 0.00 0.00 33.72 1.82
1659 2937 8.276252 TCAAACAACTTTAACAAGAGCTTAGT 57.724 30.769 0.00 0.00 33.72 2.24
1660 2938 9.736023 AATCAAACAACTTTAACAAGAGCTTAG 57.264 29.630 0.00 0.00 33.72 2.18
1662 2940 9.435688 AAAATCAAACAACTTTAACAAGAGCTT 57.564 25.926 0.00 0.00 33.72 3.74
1702 2987 7.062749 ACAAGACCATGACCGTACATATATT 57.937 36.000 0.00 0.00 0.00 1.28
1705 2990 5.353394 AACAAGACCATGACCGTACATAT 57.647 39.130 0.00 0.00 0.00 1.78
1722 3007 4.981794 ACCAAAGTCAACGAGAAAACAAG 58.018 39.130 0.00 0.00 0.00 3.16
1913 3205 6.536447 AGGAACGAGGGAGTATTTAAAAACA 58.464 36.000 0.00 0.00 0.00 2.83
1914 3206 8.552083 TTAGGAACGAGGGAGTATTTAAAAAC 57.448 34.615 0.00 0.00 0.00 2.43
1923 3215 9.597681 AGATTTATATTTAGGAACGAGGGAGTA 57.402 33.333 0.00 0.00 0.00 2.59
1924 3216 8.493787 AGATTTATATTTAGGAACGAGGGAGT 57.506 34.615 0.00 0.00 0.00 3.85
1925 3217 9.780186 AAAGATTTATATTTAGGAACGAGGGAG 57.220 33.333 0.00 0.00 0.00 4.30
1926 3218 9.555727 CAAAGATTTATATTTAGGAACGAGGGA 57.444 33.333 0.00 0.00 0.00 4.20
1927 3219 9.338622 ACAAAGATTTATATTTAGGAACGAGGG 57.661 33.333 0.00 0.00 0.00 4.30
1943 3235 9.268282 ACCTAGTGGAATCTCTACAAAGATTTA 57.732 33.333 1.05 0.00 44.16 1.40
1944 3236 8.043710 CACCTAGTGGAATCTCTACAAAGATTT 58.956 37.037 1.05 0.00 44.16 2.17
1945 3237 7.560368 CACCTAGTGGAATCTCTACAAAGATT 58.440 38.462 0.00 0.00 46.23 2.40
1946 3238 7.118496 CACCTAGTGGAATCTCTACAAAGAT 57.882 40.000 0.00 0.00 35.72 2.40
1947 3239 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
1962 3254 4.497674 GCTTCGTATGTAGTCCACCTAGTG 60.498 50.000 0.00 0.00 0.00 2.74
1963 3255 3.631227 GCTTCGTATGTAGTCCACCTAGT 59.369 47.826 0.00 0.00 0.00 2.57
1964 3256 3.630769 TGCTTCGTATGTAGTCCACCTAG 59.369 47.826 0.00 0.00 0.00 3.02
1965 3257 3.623703 TGCTTCGTATGTAGTCCACCTA 58.376 45.455 0.00 0.00 0.00 3.08
1966 3258 2.453521 TGCTTCGTATGTAGTCCACCT 58.546 47.619 0.00 0.00 0.00 4.00
1967 3259 2.953466 TGCTTCGTATGTAGTCCACC 57.047 50.000 0.00 0.00 0.00 4.61
1968 3260 5.350365 TCATTTTGCTTCGTATGTAGTCCAC 59.650 40.000 0.00 0.00 0.00 4.02
1969 3261 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
1970 3262 6.417191 TTCATTTTGCTTCGTATGTAGTCC 57.583 37.500 0.00 0.00 0.00 3.85
1971 3263 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
1972 3264 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
1973 3265 9.162793 GATTCATTCATTTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
1974 3266 8.892723 AGATTCATTCATTTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
1975 3267 7.765307 AGATTCATTCATTTTGCTTCGTATGT 58.235 30.769 0.00 0.00 0.00 2.29
1976 3268 9.162793 GTAGATTCATTCATTTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
1977 3269 8.892723 TGTAGATTCATTCATTTTGCTTCGTAT 58.107 29.630 0.00 0.00 0.00 3.06
1978 3270 8.175069 GTGTAGATTCATTCATTTTGCTTCGTA 58.825 33.333 0.00 0.00 0.00 3.43
1979 3271 7.023575 GTGTAGATTCATTCATTTTGCTTCGT 58.976 34.615 0.00 0.00 0.00 3.85
1980 3272 7.246311 AGTGTAGATTCATTCATTTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
1981 3273 8.976986 AAGTGTAGATTCATTCATTTTGCTTC 57.023 30.769 0.00 0.00 0.00 3.86
1993 3285 9.182214 ACAGATGCATTTTAAGTGTAGATTCAT 57.818 29.630 0.00 0.00 0.00 2.57
1994 3286 8.565896 ACAGATGCATTTTAAGTGTAGATTCA 57.434 30.769 0.00 0.00 0.00 2.57
2001 3293 8.840321 GGATGTATACAGATGCATTTTAAGTGT 58.160 33.333 11.91 1.15 38.38 3.55
2002 3294 8.011673 CGGATGTATACAGATGCATTTTAAGTG 58.988 37.037 11.91 0.00 38.38 3.16
2003 3295 7.715249 ACGGATGTATACAGATGCATTTTAAGT 59.285 33.333 11.91 0.00 38.38 2.24
2004 3296 8.087982 ACGGATGTATACAGATGCATTTTAAG 57.912 34.615 11.91 0.00 38.38 1.85
2005 3297 9.719355 ATACGGATGTATACAGATGCATTTTAA 57.281 29.630 11.91 0.00 38.38 1.52
2006 3298 9.150348 CATACGGATGTATACAGATGCATTTTA 57.850 33.333 11.91 0.00 38.38 1.52
2007 3299 7.661437 ACATACGGATGTATACAGATGCATTTT 59.339 33.333 12.79 0.00 44.77 1.82
2008 3300 7.118245 CACATACGGATGTATACAGATGCATTT 59.882 37.037 14.23 0.00 44.82 2.32
2009 3301 6.591448 CACATACGGATGTATACAGATGCATT 59.409 38.462 14.23 0.00 44.82 3.56
2010 3302 6.101997 CACATACGGATGTATACAGATGCAT 58.898 40.000 14.23 0.00 44.82 3.96
2011 3303 5.469479 CACATACGGATGTATACAGATGCA 58.531 41.667 14.23 0.00 44.82 3.96
2012 3304 4.864806 CCACATACGGATGTATACAGATGC 59.135 45.833 14.23 0.00 44.82 3.91
2013 3305 6.025749 ACCACATACGGATGTATACAGATG 57.974 41.667 14.23 11.05 44.82 2.90
2014 3306 6.266786 TGAACCACATACGGATGTATACAGAT 59.733 38.462 14.23 0.00 44.82 2.90
2015 3307 5.595133 TGAACCACATACGGATGTATACAGA 59.405 40.000 14.23 0.00 44.82 3.41
2016 3308 5.838529 TGAACCACATACGGATGTATACAG 58.161 41.667 14.23 0.00 44.82 2.74
2017 3309 5.855740 TGAACCACATACGGATGTATACA 57.144 39.130 14.23 8.27 44.82 2.29
2018 3310 7.600065 ACTATGAACCACATACGGATGTATAC 58.400 38.462 14.23 6.24 44.82 1.47
2019 3311 7.770366 ACTATGAACCACATACGGATGTATA 57.230 36.000 14.23 6.48 44.82 1.47
2020 3312 6.665992 ACTATGAACCACATACGGATGTAT 57.334 37.500 14.23 5.54 44.82 2.29
2021 3313 6.999871 TCTACTATGAACCACATACGGATGTA 59.000 38.462 14.23 0.00 44.82 2.29
2023 3315 6.327279 TCTACTATGAACCACATACGGATG 57.673 41.667 5.94 5.94 40.07 3.51
2024 3316 7.451877 AGAATCTACTATGAACCACATACGGAT 59.548 37.037 0.00 0.00 40.07 4.18
2025 3317 6.776116 AGAATCTACTATGAACCACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
2026 3318 6.982852 AGAATCTACTATGAACCACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
2056 3348 9.819267 CTCCTTCCGTTTCTAAATATAAGTCTT 57.181 33.333 0.00 0.00 0.00 3.01
2057 3349 8.979534 ACTCCTTCCGTTTCTAAATATAAGTCT 58.020 33.333 0.00 0.00 0.00 3.24
2064 3356 9.151177 ACCATATACTCCTTCCGTTTCTAAATA 57.849 33.333 0.00 0.00 0.00 1.40
2065 3357 8.030913 ACCATATACTCCTTCCGTTTCTAAAT 57.969 34.615 0.00 0.00 0.00 1.40
2066 3358 7.427989 ACCATATACTCCTTCCGTTTCTAAA 57.572 36.000 0.00 0.00 0.00 1.85
2067 3359 7.343833 AGAACCATATACTCCTTCCGTTTCTAA 59.656 37.037 0.00 0.00 0.00 2.10
2068 3360 6.837568 AGAACCATATACTCCTTCCGTTTCTA 59.162 38.462 0.00 0.00 0.00 2.10
2069 3361 5.661759 AGAACCATATACTCCTTCCGTTTCT 59.338 40.000 0.00 0.00 0.00 2.52
2070 3362 5.915175 AGAACCATATACTCCTTCCGTTTC 58.085 41.667 0.00 0.00 0.00 2.78
2071 3363 5.952347 AGAACCATATACTCCTTCCGTTT 57.048 39.130 0.00 0.00 0.00 3.60
2072 3364 5.952347 AAGAACCATATACTCCTTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
2073 3365 5.952347 AAAGAACCATATACTCCTTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
2074 3366 6.113411 ACAAAAGAACCATATACTCCTTCCG 58.887 40.000 0.00 0.00 0.00 4.30
2075 3367 7.393515 ACAACAAAAGAACCATATACTCCTTCC 59.606 37.037 0.00 0.00 0.00 3.46
2076 3368 8.336801 ACAACAAAAGAACCATATACTCCTTC 57.663 34.615 0.00 0.00 0.00 3.46
2077 3369 8.576442 CAACAACAAAAGAACCATATACTCCTT 58.424 33.333 0.00 0.00 0.00 3.36
2078 3370 7.724061 ACAACAACAAAAGAACCATATACTCCT 59.276 33.333 0.00 0.00 0.00 3.69
2079 3371 7.882179 ACAACAACAAAAGAACCATATACTCC 58.118 34.615 0.00 0.00 0.00 3.85
2080 3372 9.180678 CAACAACAACAAAAGAACCATATACTC 57.819 33.333 0.00 0.00 0.00 2.59
2081 3373 7.651704 GCAACAACAACAAAAGAACCATATACT 59.348 33.333 0.00 0.00 0.00 2.12
2082 3374 7.651704 AGCAACAACAACAAAAGAACCATATAC 59.348 33.333 0.00 0.00 0.00 1.47
2083 3375 7.651304 CAGCAACAACAACAAAAGAACCATATA 59.349 33.333 0.00 0.00 0.00 0.86
2137 3430 5.724239 CCACAAATGAGTTATTACGTAGCG 58.276 41.667 0.00 0.00 0.00 4.26
2246 3553 6.020995 CCGCACGACAATTAATTTATTGGTTC 60.021 38.462 18.53 9.08 39.33 3.62
2257 3564 2.739913 CCTTTCTCCGCACGACAATTAA 59.260 45.455 0.00 0.00 0.00 1.40
2298 3606 4.100344 TCCAAATGCCAGATTCATCATTGG 59.900 41.667 0.00 0.00 35.03 3.16
2304 3612 4.098894 AGGTTTCCAAATGCCAGATTCAT 58.901 39.130 0.00 0.00 0.00 2.57
2314 3622 2.099098 GGCCGTCATAGGTTTCCAAATG 59.901 50.000 0.00 0.00 0.00 2.32
2332 3640 1.645402 TAGCTGGGGAATCCAAGGCC 61.645 60.000 0.09 0.00 46.51 5.19
2392 3703 5.048713 GGAAACTTGTCGAAAATCAGTCCAT 60.049 40.000 0.00 0.00 0.00 3.41
2400 3711 4.461198 ACAGAGGGAAACTTGTCGAAAAT 58.539 39.130 0.00 0.00 0.00 1.82
2428 3739 1.702491 GGCGCAAGTATGGACCGAAC 61.702 60.000 10.83 0.00 41.68 3.95
2435 3746 0.810648 AACATGTGGCGCAAGTATGG 59.189 50.000 10.83 0.00 41.68 2.74
2474 3788 8.000780 AGTTTTTGTCTTCTTGCTCTAATGTT 57.999 30.769 0.00 0.00 0.00 2.71
2476 3790 8.778358 ACTAGTTTTTGTCTTCTTGCTCTAATG 58.222 33.333 0.00 0.00 0.00 1.90
2483 3797 4.202010 TGGCACTAGTTTTTGTCTTCTTGC 60.202 41.667 0.00 0.00 0.00 4.01
2484 3798 5.066505 AGTGGCACTAGTTTTTGTCTTCTTG 59.933 40.000 20.61 0.00 0.00 3.02
2511 3825 4.001618 GCCCTTATAAGCCAGAAGAGAG 57.998 50.000 6.99 0.00 0.00 3.20
2540 3854 8.281531 TCATTGATCAAATTAATGACCTAGGGT 58.718 33.333 13.09 0.00 39.44 4.34


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

AutoCloner maintained by Alex Coulton.