Multiple sequence alignment - TraesCS5A01G433800

Loading Multiple Alignment...

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 TraesCS5A01G433800 chr5A 100.000 2742 0 0 1 2742 617187181 617189922 0.000000e+00 5064.0
1 TraesCS5A01G433800 chr5A 86.297 1226 91 42 620 1821 617174809 617175981 0.000000e+00 1262.0
2 TraesCS5A01G433800 chr5A 95.238 357 17 0 266 622 617204483 617204839 1.430000e-157 566.0
3 TraesCS5A01G433800 chr5A 78.974 195 31 6 2302 2492 411478878 411479066 1.030000e-24 124.0
4 TraesCS5A01G433800 chr5B 89.671 1278 98 18 620 1884 610294684 610295940 0.000000e+00 1598.0
5 TraesCS5A01G433800 chr5B 90.372 457 37 4 2292 2742 610298812 610299267 6.540000e-166 593.0
6 TraesCS5A01G433800 chr5B 88.434 415 41 6 1878 2291 610298362 610298770 6.820000e-136 494.0
7 TraesCS5A01G433800 chr5B 90.080 373 31 4 253 622 610301000 610301369 1.910000e-131 479.0
8 TraesCS5A01G433800 chr5B 92.790 319 20 1 304 622 655432286 655432601 2.490000e-125 459.0
9 TraesCS5A01G433800 chr5B 84.568 324 13 17 27 313 655431803 655432126 1.240000e-73 287.0
10 TraesCS5A01G433800 chr5B 74.664 446 98 10 2301 2736 270772458 270772018 1.680000e-42 183.0
11 TraesCS5A01G433800 chr5B 74.208 442 79 26 2302 2736 366525591 366526004 4.730000e-33 152.0
12 TraesCS5A01G433800 chr5B 83.000 100 12 3 2301 2395 711816639 711816738 4.870000e-13 86.1
13 TraesCS5A01G433800 chr5D 89.538 1233 98 19 620 1848 494182655 494183860 0.000000e+00 1533.0
14 TraesCS5A01G433800 chr5D 93.041 388 22 4 240 622 494189041 494189428 1.840000e-156 562.0
15 TraesCS5A01G433800 chr5D 89.529 382 30 6 1910 2291 494184007 494184378 2.470000e-130 475.0
16 TraesCS5A01G433800 chr5D 78.797 316 45 17 2302 2608 316834681 316834983 2.790000e-45 193.0
17 TraesCS5A01G433800 chr5D 86.982 169 18 3 2397 2564 494184486 494184651 1.300000e-43 187.0
18 TraesCS5A01G433800 chr5D 90.000 110 11 0 2633 2742 494184644 494184753 2.850000e-30 143.0
19 TraesCS5A01G433800 chr4B 84.783 322 42 6 303 622 109222449 109222765 1.580000e-82 316.0
20 TraesCS5A01G433800 chr4A 80.168 358 51 16 270 617 508494597 508494250 1.630000e-62 250.0
21 TraesCS5A01G433800 chr4A 80.317 315 50 11 307 617 508358225 508357919 7.640000e-56 228.0
22 TraesCS5A01G433800 chr7B 78.667 375 73 7 2364 2733 383848145 383848517 2.730000e-60 243.0
23 TraesCS5A01G433800 chr2B 73.864 440 103 9 2291 2722 468438908 468438473 6.070000e-37 165.0
24 TraesCS5A01G433800 chr3B 80.093 216 34 9 2291 2500 729028021 729027809 4.730000e-33 152.0
25 TraesCS5A01G433800 chr3B 73.407 455 98 18 2301 2736 526193682 526194132 6.120000e-32 148.0
26 TraesCS5A01G433800 chr3D 88.636 88 6 4 2087 2172 421702725 421702640 1.340000e-18 104.0
27 TraesCS5A01G433800 chr3A 84.783 92 10 4 2087 2176 529171798 529171887 3.760000e-14 89.8
28 TraesCS5A01G433800 chr6B 96.875 32 1 0 2077 2108 240339524 240339555 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G433800 chr5A 617187181 617189922 2741 False 5064.0 5064 100.00000 1 2742 1 chr5A.!!$F3 2741
1 TraesCS5A01G433800 chr5A 617174809 617175981 1172 False 1262.0 1262 86.29700 620 1821 1 chr5A.!!$F2 1201
2 TraesCS5A01G433800 chr5B 610294684 610301369 6685 False 791.0 1598 89.63925 253 2742 4 chr5B.!!$F3 2489
3 TraesCS5A01G433800 chr5B 655431803 655432601 798 False 373.0 459 88.67900 27 622 2 chr5B.!!$F4 595
4 TraesCS5A01G433800 chr5D 494182655 494184753 2098 False 584.5 1533 89.01225 620 2742 4 chr5D.!!$F3 2122

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
71 73 0.1791 TCAGCATCTTAGCTCACGGC 60.179 55.0 0.0 0.0 44.54 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2029 0.384309 TCTGCCATGTCCGATCGTAC 59.616 55.0 15.09 9.39 0.0 3.67 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
35 36 8.470805 TCTCACTATAACTAGCCTGAAAGAAAG 58.529 37.037 0.00 0.00 34.07 2.62
37 38 8.812972 TCACTATAACTAGCCTGAAAGAAAGAA 58.187 33.333 0.00 0.00 34.07 2.52
49 50 6.015027 TGAAAGAAAGAAACGAACAAACCA 57.985 33.333 0.00 0.00 0.00 3.67
55 56 5.424121 AAGAAACGAACAAACCATCTCAG 57.576 39.130 0.00 0.00 0.00 3.35
60 61 3.005554 CGAACAAACCATCTCAGCATCT 58.994 45.455 0.00 0.00 0.00 2.90
71 73 0.179100 TCAGCATCTTAGCTCACGGC 60.179 55.000 0.00 0.00 44.54 5.68
74 76 1.086696 GCATCTTAGCTCACGGCAAA 58.913 50.000 0.00 0.00 44.79 3.68
111 114 7.432148 TCAAGATTCCTAGCCACAATTAGTA 57.568 36.000 0.00 0.00 0.00 1.82
123 131 3.921677 ACAATTAGTAGTGTGACCGTGG 58.078 45.455 0.00 0.00 30.16 4.94
189 205 3.371487 CCATCTATAAACACAGCCCACCA 60.371 47.826 0.00 0.00 0.00 4.17
209 225 1.079543 CTGCACCGCTGAGCTTACT 60.080 57.895 1.78 0.00 0.00 2.24
213 229 0.179108 CACCGCTGAGCTTACTACCC 60.179 60.000 1.78 0.00 0.00 3.69
214 230 0.613853 ACCGCTGAGCTTACTACCCA 60.614 55.000 1.78 0.00 0.00 4.51
215 231 0.179108 CCGCTGAGCTTACTACCCAC 60.179 60.000 1.78 0.00 0.00 4.61
217 233 0.902531 GCTGAGCTTACTACCCACCA 59.097 55.000 0.00 0.00 0.00 4.17
219 235 2.483889 GCTGAGCTTACTACCCACCATC 60.484 54.545 0.00 0.00 0.00 3.51
220 236 1.754803 TGAGCTTACTACCCACCATCG 59.245 52.381 0.00 0.00 0.00 3.84
224 240 2.550978 CTTACTACCCACCATCGCAAG 58.449 52.381 0.00 0.00 0.00 4.01
225 241 0.828022 TACTACCCACCATCGCAAGG 59.172 55.000 0.00 0.00 38.47 3.61
264 296 1.443194 GCACACAGCAAATGGAGCG 60.443 57.895 0.00 0.00 44.79 5.03
284 322 3.793144 GCCAAGAAGCGCTGTCCG 61.793 66.667 12.58 0.00 40.75 4.79
302 340 2.642700 CAAAGAAACCGGCCGTGG 59.357 61.111 26.12 12.62 0.00 4.94
433 640 3.267860 CTGCTCGCCTTCATCCGC 61.268 66.667 0.00 0.00 0.00 5.54
461 668 4.966787 TGCCGCACCCTTGGTTCC 62.967 66.667 0.00 0.00 31.02 3.62
1186 1411 3.460672 ATGGGCTACATGTCGGGCG 62.461 63.158 0.00 0.00 38.70 6.13
1400 1646 0.162933 ACATTGCGCAAGTACGAACG 59.837 50.000 28.62 10.77 41.68 3.95
1502 1748 2.353607 GATCCAGACGCTACGCCG 60.354 66.667 0.00 0.00 0.00 6.46
1572 1822 1.005275 AGATGATCGGAGCGCATGG 60.005 57.895 11.47 0.00 0.00 3.66
1680 1930 1.569479 GGGAACGTCAACAGAGCAGC 61.569 60.000 0.00 0.00 0.00 5.25
1719 1975 3.238241 CGTCGCCGTCGTAGCAAG 61.238 66.667 0.00 0.00 36.96 4.01
1720 1976 2.879462 GTCGCCGTCGTAGCAAGG 60.879 66.667 0.00 0.00 36.96 3.61
1752 2008 0.035458 GGACCCTGACACCTGTTGAG 59.965 60.000 0.00 0.00 0.00 3.02
1773 2029 3.196648 GCCACGGGCCTGTAAATG 58.803 61.111 19.20 4.71 44.06 2.32
1774 2030 1.677633 GCCACGGGCCTGTAAATGT 60.678 57.895 19.20 0.00 44.06 2.71
1775 2031 0.393267 GCCACGGGCCTGTAAATGTA 60.393 55.000 19.20 0.00 44.06 2.29
1776 2032 1.375551 CCACGGGCCTGTAAATGTAC 58.624 55.000 19.20 0.00 0.00 2.90
1777 2033 1.003851 CACGGGCCTGTAAATGTACG 58.996 55.000 19.20 2.59 32.40 3.67
1781 2037 2.132762 GGGCCTGTAAATGTACGATCG 58.867 52.381 14.88 14.88 32.40 3.69
1809 2074 0.620700 AGAGGCCAAGACCCCGTTAT 60.621 55.000 5.01 0.00 0.00 1.89
1878 2144 1.064685 GGGGGATCTCGTTGGTCATTT 60.065 52.381 0.00 0.00 0.00 2.32
1880 2146 1.401905 GGGATCTCGTTGGTCATTTGC 59.598 52.381 0.00 0.00 0.00 3.68
1881 2147 2.083774 GGATCTCGTTGGTCATTTGCA 58.916 47.619 0.00 0.00 0.00 4.08
1882 2148 2.159517 GGATCTCGTTGGTCATTTGCAC 60.160 50.000 0.00 0.00 0.00 4.57
1883 2149 2.254546 TCTCGTTGGTCATTTGCACT 57.745 45.000 0.00 0.00 0.00 4.40
1898 4591 4.846779 TTGCACTAAAGTGGTCAAATCC 57.153 40.909 11.86 0.00 45.72 3.01
1901 4594 3.689649 GCACTAAAGTGGTCAAATCCGAT 59.310 43.478 11.86 0.00 45.72 4.18
1983 4676 5.712917 TGTTCTCTTTTACAACCACAACCTT 59.287 36.000 0.00 0.00 0.00 3.50
2027 4720 3.351740 TCCAAATACATGCACGTCCATT 58.648 40.909 0.00 0.00 0.00 3.16
2056 4749 9.546428 TTGATAATACATGATAACAGTGAGTGG 57.454 33.333 0.00 0.00 0.00 4.00
2068 4761 3.961408 ACAGTGAGTGGATACCTCATACC 59.039 47.826 0.00 0.00 42.97 2.73
2188 4881 6.313905 CCCGCATATACTCCACAAGATAATTC 59.686 42.308 0.00 0.00 0.00 2.17
2189 4882 6.313905 CCGCATATACTCCACAAGATAATTCC 59.686 42.308 0.00 0.00 0.00 3.01
2223 4917 3.181454 ACCTGTTGGTCTCGAAATTGTCT 60.181 43.478 0.00 0.00 44.78 3.41
2253 4947 1.632589 AGAAAGTTCCCAACATGCCC 58.367 50.000 0.00 0.00 0.00 5.36
2254 4948 0.608130 GAAAGTTCCCAACATGCCCC 59.392 55.000 0.00 0.00 0.00 5.80
2255 4949 0.105246 AAAGTTCCCAACATGCCCCA 60.105 50.000 0.00 0.00 0.00 4.96
2274 4968 3.306364 CCCACATCTTATTCTAGGAGGCG 60.306 52.174 0.00 0.00 0.00 5.52
2279 4973 3.912248 TCTTATTCTAGGAGGCGGACTT 58.088 45.455 0.00 0.00 0.00 3.01
2285 4979 2.100989 CTAGGAGGCGGACTTGTACTT 58.899 52.381 0.00 0.00 0.00 2.24
2291 4985 1.066136 GCGGACTTGTACTTCGAACC 58.934 55.000 0.00 0.00 0.00 3.62
2351 5092 0.038618 GCCACAATGTTTCGGTTCCC 60.039 55.000 0.00 0.00 0.00 3.97
2372 5113 2.279741 GCATCATTGTAGCTCCACGAA 58.720 47.619 0.00 0.00 0.00 3.85
2384 5125 2.944094 GCTCCACGAACAATACCCCAAT 60.944 50.000 0.00 0.00 0.00 3.16
2417 5158 3.143728 ACACCGAATACCCTTTTCACAC 58.856 45.455 0.00 0.00 0.00 3.82
2419 5160 4.040706 ACACCGAATACCCTTTTCACACTA 59.959 41.667 0.00 0.00 0.00 2.74
2475 5216 0.252558 TCTTTCCTACCTCGGGGCTT 60.253 55.000 0.00 0.00 35.63 4.35
2476 5217 0.618981 CTTTCCTACCTCGGGGCTTT 59.381 55.000 0.00 0.00 35.63 3.51
2477 5218 0.326927 TTTCCTACCTCGGGGCTTTG 59.673 55.000 0.00 0.00 35.63 2.77
2537 5280 3.385749 ATCGCAAGGTAGCACCCCG 62.386 63.158 0.00 3.89 39.75 5.73
2559 5302 6.148811 CCCGTTGTATAGTTGTGTCTTTTGAT 59.851 38.462 0.00 0.00 0.00 2.57
2572 5315 6.710295 TGTGTCTTTTGATAGTGTAGTTGCAT 59.290 34.615 0.00 0.00 0.00 3.96
2576 5319 6.531594 TCTTTTGATAGTGTAGTTGCATCTCG 59.468 38.462 0.00 0.00 0.00 4.04
2586 5329 2.976903 GCATCTCGGAGCATGCCC 60.977 66.667 15.66 14.37 39.70 5.36
2608 5351 4.202040 CCATTGCAAGTCTCTTGAACAACA 60.202 41.667 4.94 0.00 0.00 3.33
2611 5354 4.454678 TGCAAGTCTCTTGAACAACAGAT 58.545 39.130 12.77 0.00 0.00 2.90
2614 5357 6.369890 TGCAAGTCTCTTGAACAACAGATATC 59.630 38.462 12.77 0.00 0.00 1.63
2645 5388 8.026341 AGCATATTGATATCATTGTGAGAACG 57.974 34.615 21.53 2.27 0.00 3.95
2682 5427 3.177228 AGTCTGCCTAATCCACAAGTCT 58.823 45.455 0.00 0.00 0.00 3.24
2686 5431 5.938125 GTCTGCCTAATCCACAAGTCTTTTA 59.062 40.000 0.00 0.00 0.00 1.52
2693 5438 8.960591 CCTAATCCACAAGTCTTTTAATGTCAT 58.039 33.333 0.00 0.00 0.00 3.06
2709 5454 8.800370 TTAATGTCATTGCTTCAAGTATGGTA 57.200 30.769 8.39 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.563748 AGGCTAGTTATAGTGAGAGTAACTTAG 57.436 37.037 2.79 1.54 38.95 2.18
1 2 9.339850 CAGGCTAGTTATAGTGAGAGTAACTTA 57.660 37.037 2.79 0.00 38.95 2.24
2 3 8.053963 TCAGGCTAGTTATAGTGAGAGTAACTT 58.946 37.037 2.79 0.00 38.95 2.66
3 4 7.575505 TCAGGCTAGTTATAGTGAGAGTAACT 58.424 38.462 0.00 0.00 40.60 2.24
4 5 7.804843 TCAGGCTAGTTATAGTGAGAGTAAC 57.195 40.000 0.00 0.00 0.00 2.50
5 6 8.818622 TTTCAGGCTAGTTATAGTGAGAGTAA 57.181 34.615 0.00 0.00 0.00 2.24
6 7 8.272889 TCTTTCAGGCTAGTTATAGTGAGAGTA 58.727 37.037 0.00 0.00 0.00 2.59
7 8 7.120051 TCTTTCAGGCTAGTTATAGTGAGAGT 58.880 38.462 0.00 0.00 0.00 3.24
8 9 7.575414 TCTTTCAGGCTAGTTATAGTGAGAG 57.425 40.000 0.00 0.00 0.00 3.20
9 10 7.956328 TTCTTTCAGGCTAGTTATAGTGAGA 57.044 36.000 0.00 0.00 0.00 3.27
10 11 8.470805 TCTTTCTTTCAGGCTAGTTATAGTGAG 58.529 37.037 0.00 0.00 0.00 3.51
11 12 8.362464 TCTTTCTTTCAGGCTAGTTATAGTGA 57.638 34.615 0.00 0.00 0.00 3.41
12 13 9.436957 TTTCTTTCTTTCAGGCTAGTTATAGTG 57.563 33.333 0.00 0.00 0.00 2.74
13 14 9.438228 GTTTCTTTCTTTCAGGCTAGTTATAGT 57.562 33.333 0.00 0.00 0.00 2.12
14 15 8.596380 CGTTTCTTTCTTTCAGGCTAGTTATAG 58.404 37.037 0.00 0.00 0.00 1.31
15 16 8.308931 TCGTTTCTTTCTTTCAGGCTAGTTATA 58.691 33.333 0.00 0.00 0.00 0.98
16 17 7.159372 TCGTTTCTTTCTTTCAGGCTAGTTAT 58.841 34.615 0.00 0.00 0.00 1.89
17 18 6.518493 TCGTTTCTTTCTTTCAGGCTAGTTA 58.482 36.000 0.00 0.00 0.00 2.24
18 19 5.365619 TCGTTTCTTTCTTTCAGGCTAGTT 58.634 37.500 0.00 0.00 0.00 2.24
19 20 4.957296 TCGTTTCTTTCTTTCAGGCTAGT 58.043 39.130 0.00 0.00 0.00 2.57
20 21 5.236478 TGTTCGTTTCTTTCTTTCAGGCTAG 59.764 40.000 0.00 0.00 0.00 3.42
21 22 5.120399 TGTTCGTTTCTTTCTTTCAGGCTA 58.880 37.500 0.00 0.00 0.00 3.93
22 23 3.945285 TGTTCGTTTCTTTCTTTCAGGCT 59.055 39.130 0.00 0.00 0.00 4.58
23 24 4.287238 TGTTCGTTTCTTTCTTTCAGGC 57.713 40.909 0.00 0.00 0.00 4.85
24 25 5.515270 GGTTTGTTCGTTTCTTTCTTTCAGG 59.485 40.000 0.00 0.00 0.00 3.86
25 26 6.090129 TGGTTTGTTCGTTTCTTTCTTTCAG 58.910 36.000 0.00 0.00 0.00 3.02
35 36 3.003275 TGCTGAGATGGTTTGTTCGTTTC 59.997 43.478 0.00 0.00 0.00 2.78
37 38 2.571212 TGCTGAGATGGTTTGTTCGTT 58.429 42.857 0.00 0.00 0.00 3.85
49 50 2.035704 CCGTGAGCTAAGATGCTGAGAT 59.964 50.000 0.00 0.00 44.17 2.75
55 56 1.086696 TTTGCCGTGAGCTAAGATGC 58.913 50.000 0.00 0.00 44.23 3.91
60 61 3.396260 AGTAAGTTTGCCGTGAGCTAA 57.604 42.857 0.00 0.00 44.23 3.09
123 131 1.845809 CGCCTGCTCTGTTTGACCAC 61.846 60.000 0.00 0.00 0.00 4.16
209 225 2.270850 GCCTTGCGATGGTGGGTA 59.729 61.111 0.00 0.00 0.00 3.69
215 231 4.883354 GAGGGGGCCTTGCGATGG 62.883 72.222 0.84 0.00 31.76 3.51
217 233 3.483869 GAGAGGGGGCCTTGCGAT 61.484 66.667 0.84 0.00 31.76 4.58
220 236 3.468326 GATCGAGAGGGGGCCTTGC 62.468 68.421 0.84 0.00 31.76 4.01
224 240 3.934962 GCTGATCGAGAGGGGGCC 61.935 72.222 0.00 0.00 0.00 5.80
225 241 3.157252 TGCTGATCGAGAGGGGGC 61.157 66.667 0.00 0.00 0.00 5.80
230 262 1.141234 TGCTGCTGCTGATCGAGAG 59.859 57.895 17.00 0.00 40.48 3.20
279 317 2.548295 GCCGGTTTCTTTGCGGACA 61.548 57.895 1.90 0.00 0.00 4.02
284 322 2.050442 CACGGCCGGTTTCTTTGC 60.050 61.111 31.76 0.00 0.00 3.68
454 661 2.354729 CAGATGGCCCGGAACCAA 59.645 61.111 18.63 4.55 41.49 3.67
539 746 4.849329 CACGTACCCGAGCTCCGC 62.849 72.222 8.47 0.00 37.88 5.54
540 747 4.849329 GCACGTACCCGAGCTCCG 62.849 72.222 8.47 7.98 45.51 4.63
615 822 3.430862 CAACCACCATGACCGCGG 61.431 66.667 26.86 26.86 0.00 6.46
616 823 4.101790 GCAACCACCATGACCGCG 62.102 66.667 0.00 0.00 0.00 6.46
617 824 4.101790 CGCAACCACCATGACCGC 62.102 66.667 0.00 0.00 0.00 5.68
618 825 4.101790 GCGCAACCACCATGACCG 62.102 66.667 0.30 0.00 0.00 4.79
619 826 4.101790 CGCGCAACCACCATGACC 62.102 66.667 8.75 0.00 0.00 4.02
620 827 2.612567 TTCGCGCAACCACCATGAC 61.613 57.895 8.75 0.00 0.00 3.06
621 828 2.281139 TTCGCGCAACCACCATGA 60.281 55.556 8.75 0.00 0.00 3.07
972 1179 4.083110 CCTGCTGTAATTCTTCCTTGTGTG 60.083 45.833 0.00 0.00 0.00 3.82
1375 1600 1.128692 GTACTTGCGCAATGTGGACTC 59.871 52.381 25.26 5.03 0.00 3.36
1400 1646 3.715628 ATTTTCTGCACTTGTGGTGTC 57.284 42.857 2.81 0.00 46.86 3.67
1412 1658 1.195900 TGGCACGACGTTATTTTCTGC 59.804 47.619 0.00 0.00 0.00 4.26
1413 1659 3.740044 ATGGCACGACGTTATTTTCTG 57.260 42.857 0.00 0.00 0.00 3.02
1461 1707 2.202492 CGTCGCCGGAGAAGACAG 60.202 66.667 15.65 6.34 34.46 3.51
1502 1748 3.121030 CTGCTGCACGTACCTGCC 61.121 66.667 13.31 1.19 36.21 4.85
1533 1783 0.450184 CACGGGCCTATTCCAAAACG 59.550 55.000 0.84 0.00 0.00 3.60
1572 1822 1.951631 GCTCCGATTAGCTCACCGC 60.952 63.158 0.00 0.00 39.50 5.68
1680 1930 1.674221 CGAAGGCCAGACTTCTCCTTG 60.674 57.143 5.01 0.00 43.61 3.61
1719 1975 2.126031 GTCCACGAACGAGAGCCC 60.126 66.667 0.14 0.00 0.00 5.19
1720 1976 2.126031 GGTCCACGAACGAGAGCC 60.126 66.667 0.14 0.00 0.00 4.70
1726 1982 1.663702 GTGTCAGGGTCCACGAACG 60.664 63.158 0.00 0.00 0.00 3.95
1727 1983 1.301479 GGTGTCAGGGTCCACGAAC 60.301 63.158 0.00 0.00 32.30 3.95
1773 2029 0.384309 TCTGCCATGTCCGATCGTAC 59.616 55.000 15.09 9.39 0.00 3.67
1774 2030 0.668535 CTCTGCCATGTCCGATCGTA 59.331 55.000 15.09 0.00 0.00 3.43
1775 2031 1.439228 CTCTGCCATGTCCGATCGT 59.561 57.895 15.09 0.00 0.00 3.73
1776 2032 1.300465 CCTCTGCCATGTCCGATCG 60.300 63.158 8.51 8.51 0.00 3.69
1777 2033 1.596477 GCCTCTGCCATGTCCGATC 60.596 63.158 0.00 0.00 0.00 3.69
1797 2062 2.871096 TTCAAGCATAACGGGGTCTT 57.129 45.000 0.00 0.00 0.00 3.01
1829 2095 1.468565 CCGTTCATTCAAGCCATGCTG 60.469 52.381 0.00 0.00 39.62 4.41
1862 2128 2.744202 AGTGCAAATGACCAACGAGATC 59.256 45.455 0.00 0.00 0.00 2.75
1863 2129 2.783135 AGTGCAAATGACCAACGAGAT 58.217 42.857 0.00 0.00 0.00 2.75
1878 2144 2.811431 CGGATTTGACCACTTTAGTGCA 59.189 45.455 4.34 0.00 44.34 4.57
1880 2146 4.437390 GCATCGGATTTGACCACTTTAGTG 60.437 45.833 2.86 2.86 45.23 2.74
1881 2147 3.689649 GCATCGGATTTGACCACTTTAGT 59.310 43.478 0.00 0.00 0.00 2.24
1882 2148 3.689161 TGCATCGGATTTGACCACTTTAG 59.311 43.478 0.00 0.00 0.00 1.85
1883 2149 3.438781 GTGCATCGGATTTGACCACTTTA 59.561 43.478 0.00 0.00 0.00 1.85
1954 4647 4.022329 GTGGTTGTAAAAGAGAACATGGGG 60.022 45.833 0.00 0.00 32.91 4.96
2117 4810 7.565450 TTTCATGTTTGAATTATGCACTTCG 57.435 32.000 0.00 0.00 41.38 3.79
2157 4850 2.038557 GTGGAGTATATGCGGGTCCAAT 59.961 50.000 2.46 0.00 39.02 3.16
2223 4917 8.603898 TGTTGGGAACTTTCTAGAGATACATA 57.396 34.615 0.00 0.00 0.00 2.29
2243 4937 2.142356 TAAGATGTGGGGCATGTTGG 57.858 50.000 0.00 0.00 40.66 3.77
2253 4947 3.306364 CCGCCTCCTAGAATAAGATGTGG 60.306 52.174 0.00 0.00 0.00 4.17
2254 4948 3.574396 TCCGCCTCCTAGAATAAGATGTG 59.426 47.826 0.00 0.00 0.00 3.21
2255 4949 3.574826 GTCCGCCTCCTAGAATAAGATGT 59.425 47.826 0.00 0.00 0.00 3.06
2274 4968 2.298163 TGGAGGTTCGAAGTACAAGTCC 59.702 50.000 0.00 0.00 0.00 3.85
2279 4973 0.599558 CCGTGGAGGTTCGAAGTACA 59.400 55.000 0.00 0.00 34.51 2.90
2285 4979 3.000819 ATGGCCGTGGAGGTTCGA 61.001 61.111 0.00 0.00 43.70 3.71
2291 4985 0.321210 TGTACAACATGGCCGTGGAG 60.321 55.000 28.37 21.17 0.00 3.86
2351 5092 0.578683 CGTGGAGCTACAATGATGCG 59.421 55.000 0.00 0.00 0.00 4.73
2384 5125 1.334160 TTCGGTGTACTCCAAGCTCA 58.666 50.000 14.09 0.00 0.00 4.26
2417 5158 6.690194 AATGCAAGAAGGTGCTAGAAATAG 57.310 37.500 0.00 0.00 45.17 1.73
2419 5160 5.244626 ACAAATGCAAGAAGGTGCTAGAAAT 59.755 36.000 0.00 0.00 45.17 2.17
2457 5198 0.618981 AAAGCCCCGAGGTAGGAAAG 59.381 55.000 0.00 0.00 34.57 2.62
2475 5216 5.357257 GGCTTTCGTGAAGACTATATCCAA 58.643 41.667 5.66 0.00 40.48 3.53
2476 5217 4.499188 CGGCTTTCGTGAAGACTATATCCA 60.499 45.833 5.66 0.00 41.56 3.41
2477 5218 3.982058 CGGCTTTCGTGAAGACTATATCC 59.018 47.826 5.66 0.00 41.56 2.59
2508 5250 4.082190 GCTACCTTGCGATGGTATCTATCA 60.082 45.833 3.34 0.00 39.10 2.15
2559 5302 2.099263 GCTCCGAGATGCAACTACACTA 59.901 50.000 0.00 0.00 0.00 2.74
2572 5315 1.153107 CAATGGGCATGCTCCGAGA 60.153 57.895 16.70 0.00 0.00 4.04
2586 5329 4.923893 TGTTGTTCAAGAGACTTGCAATG 58.076 39.130 0.00 0.00 0.00 2.82
2608 5351 5.611128 ATCAATATGCTCCAGCGATATCT 57.389 39.130 0.34 0.00 45.83 1.98
2611 5354 6.469782 TGATATCAATATGCTCCAGCGATA 57.530 37.500 1.98 0.00 45.83 2.92
2614 5357 5.353400 ACAATGATATCAATATGCTCCAGCG 59.647 40.000 9.99 0.00 45.83 5.18
2645 5388 2.094854 CAGACTTTCTTTGGCATGCCTC 60.095 50.000 35.53 22.10 36.94 4.70
2682 5427 8.584157 ACCATACTTGAAGCAATGACATTAAAA 58.416 29.630 0.00 0.00 0.00 1.52
2686 5431 6.886459 ACTACCATACTTGAAGCAATGACATT 59.114 34.615 9.06 0.00 0.00 2.71
2693 5438 3.343617 GCCACTACCATACTTGAAGCAA 58.656 45.455 0.00 0.00 0.00 3.91
2709 5454 0.398318 GTCACTCCAAAGAGGCCACT 59.602 55.000 5.01 0.00 45.11 4.00


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

AutoCloner maintained by Alex Coulton.