Multiple sequence alignment - TraesCS6B01G351800

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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 TraesCS6B01G351800 chr6B 100.000 2291 0 0 1 2291 617127423 617129713 0.000000e+00 4231.0
1 TraesCS6B01G351800 chr6D 85.927 2146 158 50 78 2123 410174535 410176636 0.000000e+00 2158.0
2 TraesCS6B01G351800 chr6D 83.550 231 34 3 2024 2251 410220248 410220477 1.780000e-51 213.0
3 TraesCS6B01G351800 chr6A 90.334 1407 69 26 495 1845 555672905 555674300 0.000000e+00 1783.0
4 TraesCS6B01G351800 chr6A 85.882 425 41 11 1836 2254 555674360 555674771 3.500000e-118 435.0
5 TraesCS6B01G351800 chr6A 86.316 285 5 12 208 469 555672571 555672844 1.730000e-71 279.0
6 TraesCS6B01G351800 chr7D 78.198 555 76 27 1087 1638 563707857 563708369 1.710000e-81 313.0
7 TraesCS6B01G351800 chr7B 74.490 490 62 32 1121 1603 614229252 614228819 1.100000e-33 154.0
8 TraesCS6B01G351800 chr4A 96.364 55 1 1 10 64 581761269 581761216 3.130000e-14 89.8


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 TraesCS6B01G351800 chr6B 617127423 617129713 2290 False 4231.000000 4231 100.000000 1 2291 1 chr6B.!!$F1 2290
1 TraesCS6B01G351800 chr6D 410174535 410176636 2101 False 2158.000000 2158 85.927000 78 2123 1 chr6D.!!$F1 2045
2 TraesCS6B01G351800 chr6A 555672571 555674771 2200 False 832.333333 1783 87.510667 208 2254 3 chr6A.!!$F1 2046
3 TraesCS6B01G351800 chr7D 563707857 563708369 512 False 313.000000 313 78.198000 1087 1638 1 chr7D.!!$F1 551

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
589 693 0.179137 CAAGCTAGCGATCGGACACA 60.179 55.0 18.3 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2485 0.034863 TATTGAAACCTGGGCCCGTC 60.035 55.0 19.37 9.71 0.0 4.79 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
23 24 6.287107 GGACACTGATGTATTTCCGTTATG 57.713 41.667 0.00 0.00 39.95 1.90
24 25 5.815740 GGACACTGATGTATTTCCGTTATGT 59.184 40.000 0.00 0.00 39.95 2.29
25 26 6.018994 GGACACTGATGTATTTCCGTTATGTC 60.019 42.308 0.00 0.00 39.95 3.06
26 27 6.403049 ACACTGATGTATTTCCGTTATGTCA 58.597 36.000 0.00 0.00 37.26 3.58
27 28 6.312918 ACACTGATGTATTTCCGTTATGTCAC 59.687 38.462 0.00 0.00 37.26 3.67
28 29 5.518847 ACTGATGTATTTCCGTTATGTCACG 59.481 40.000 0.00 0.00 40.02 4.35
39 40 5.138800 CGTTATGTCACGGTAATGGAAAG 57.861 43.478 0.00 0.00 36.47 2.62
40 41 4.033587 CGTTATGTCACGGTAATGGAAAGG 59.966 45.833 0.00 0.00 36.47 3.11
41 42 2.483014 TGTCACGGTAATGGAAAGGG 57.517 50.000 0.00 0.00 0.00 3.95
42 43 1.003812 TGTCACGGTAATGGAAAGGGG 59.996 52.381 0.00 0.00 0.00 4.79
43 44 1.003928 GTCACGGTAATGGAAAGGGGT 59.996 52.381 0.00 0.00 0.00 4.95
44 45 1.706305 TCACGGTAATGGAAAGGGGTT 59.294 47.619 0.00 0.00 0.00 4.11
45 46 2.911636 TCACGGTAATGGAAAGGGGTTA 59.088 45.455 0.00 0.00 0.00 2.85
46 47 3.524380 TCACGGTAATGGAAAGGGGTTAT 59.476 43.478 0.00 0.00 0.00 1.89
47 48 3.630312 CACGGTAATGGAAAGGGGTTATG 59.370 47.826 0.00 0.00 0.00 1.90
48 49 2.621526 CGGTAATGGAAAGGGGTTATGC 59.378 50.000 0.00 0.00 0.00 3.14
49 50 2.963101 GGTAATGGAAAGGGGTTATGCC 59.037 50.000 0.00 0.00 0.00 4.40
84 85 5.767816 AAAGAACCTAGCGTGAAAAATGT 57.232 34.783 0.00 0.00 0.00 2.71
96 97 5.116983 GCGTGAAAAATGTTCGATTTGTCAT 59.883 36.000 6.22 0.00 37.51 3.06
105 106 6.266168 TGTTCGATTTGTCATGCCTAAAAT 57.734 33.333 0.00 0.00 0.00 1.82
112 113 6.647334 TTTGTCATGCCTAAAATTCTGACA 57.353 33.333 0.00 0.00 40.69 3.58
116 117 6.433716 TGTCATGCCTAAAATTCTGACATTCA 59.566 34.615 0.00 0.00 38.36 2.57
144 145 9.527157 TGAATATTCAGGTCCTTACAATGAAAA 57.473 29.630 14.23 0.00 36.80 2.29
173 174 3.734683 CACAACTAGTGCACGCTTG 57.265 52.632 12.01 15.49 42.15 4.01
174 175 1.217001 CACAACTAGTGCACGCTTGA 58.783 50.000 22.94 5.14 42.15 3.02
175 176 1.597195 CACAACTAGTGCACGCTTGAA 59.403 47.619 22.94 3.85 42.15 2.69
176 177 2.031560 CACAACTAGTGCACGCTTGAAA 59.968 45.455 22.94 2.40 42.15 2.69
177 178 2.680841 ACAACTAGTGCACGCTTGAAAA 59.319 40.909 22.94 1.25 0.00 2.29
178 179 3.127895 ACAACTAGTGCACGCTTGAAAAA 59.872 39.130 22.94 0.39 0.00 1.94
295 307 2.027073 CGCACGCACACTGGTACAT 61.027 57.895 0.00 0.00 38.20 2.29
311 323 4.243270 GGTACATATGGCGGTATCAACTC 58.757 47.826 7.80 0.00 0.00 3.01
325 338 1.002366 CAACTCCGATCCGCTGAAAG 58.998 55.000 0.00 0.00 0.00 2.62
483 532 7.819415 CACGACTGACAATATGATATAACCCAT 59.181 37.037 0.00 0.00 0.00 4.00
500 553 2.517959 CCATCACCTGGTGTGTCATTT 58.482 47.619 25.15 1.90 45.61 2.32
543 642 2.292292 GCTCGGTGGACTAATCTCTCTC 59.708 54.545 0.00 0.00 0.00 3.20
572 676 4.314522 TTTGCTATCTGGAATGGACCAA 57.685 40.909 0.00 0.00 39.59 3.67
585 689 1.734137 GACCAAGCTAGCGATCGGA 59.266 57.895 18.30 0.00 0.00 4.55
586 690 0.595310 GACCAAGCTAGCGATCGGAC 60.595 60.000 18.30 10.35 0.00 4.79
587 691 1.320344 ACCAAGCTAGCGATCGGACA 61.320 55.000 18.30 0.00 0.00 4.02
588 692 0.872021 CCAAGCTAGCGATCGGACAC 60.872 60.000 18.30 0.00 0.00 3.67
589 693 0.179137 CAAGCTAGCGATCGGACACA 60.179 55.000 18.30 0.00 0.00 3.72
590 694 0.530744 AAGCTAGCGATCGGACACAA 59.469 50.000 18.30 0.00 0.00 3.33
651 763 1.196808 CGTCCGCAGCAAAAATGTACT 59.803 47.619 0.00 0.00 0.00 2.73
652 764 2.413796 CGTCCGCAGCAAAAATGTACTA 59.586 45.455 0.00 0.00 0.00 1.82
653 765 3.063452 CGTCCGCAGCAAAAATGTACTAT 59.937 43.478 0.00 0.00 0.00 2.12
719 832 3.405093 ATCGGGCATGCACGGATGT 62.405 57.895 39.29 21.32 43.94 3.06
732 845 1.341679 ACGGATGTAGTCACCAGGCTA 60.342 52.381 0.00 0.00 0.00 3.93
773 886 7.311408 CAAGCATCGAATCTGATGATAGACTA 58.689 38.462 15.48 0.00 43.70 2.59
776 889 6.624642 GCATCGAATCTGATGATAGACTAGCA 60.625 42.308 15.48 2.34 46.98 3.49
807 920 0.390860 AAGCAGCCGATATCTTCGCT 59.609 50.000 0.34 2.30 46.71 4.93
860 973 1.952133 CCGAAACGTGAGGCAACGA 60.952 57.895 17.89 0.00 46.49 3.85
880 993 1.003118 AGAGTGCCCGTAAAAGCATGA 59.997 47.619 0.00 0.00 41.86 3.07
882 995 1.539827 AGTGCCCGTAAAAGCATGAAC 59.460 47.619 0.00 0.00 41.86 3.18
883 996 1.539827 GTGCCCGTAAAAGCATGAACT 59.460 47.619 0.00 0.00 41.86 3.01
884 997 2.030274 GTGCCCGTAAAAGCATGAACTT 60.030 45.455 0.00 0.00 41.86 2.66
885 998 2.625790 TGCCCGTAAAAGCATGAACTTT 59.374 40.909 0.00 0.00 41.60 2.66
886 999 2.986479 GCCCGTAAAAGCATGAACTTTG 59.014 45.455 0.00 0.00 39.76 2.77
887 1000 3.552068 GCCCGTAAAAGCATGAACTTTGT 60.552 43.478 0.00 0.00 39.76 2.83
888 1001 4.226761 CCCGTAAAAGCATGAACTTTGTC 58.773 43.478 0.00 0.00 39.76 3.18
889 1002 4.261405 CCCGTAAAAGCATGAACTTTGTCA 60.261 41.667 0.00 0.00 39.76 3.58
901 1016 3.558931 ACTTTGTCATCGCCATGGATA 57.441 42.857 18.40 1.65 0.00 2.59
917 1032 7.415318 CGCCATGGATATCGGGTATATATAGAC 60.415 44.444 18.40 0.00 30.53 2.59
983 1098 3.766051 TCTGTCTGAGAGAGCAAAGCATA 59.234 43.478 1.08 0.00 0.00 3.14
984 1099 3.854666 TGTCTGAGAGAGCAAAGCATAC 58.145 45.455 0.00 0.00 0.00 2.39
985 1100 3.259123 TGTCTGAGAGAGCAAAGCATACA 59.741 43.478 0.00 0.00 0.00 2.29
998 1133 5.391950 GCAAAGCATACAAAAGATCGAGGAA 60.392 40.000 0.00 0.00 0.00 3.36
1301 1436 2.279784 CGCCTAGCCTAGCACTGC 60.280 66.667 0.00 0.00 0.00 4.40
1337 1481 6.257423 CAATAATCTCTCTCTGATCGATCCG 58.743 44.000 22.31 16.29 0.00 4.18
1390 1553 4.527157 GCGATTGCTCGTGGCTGC 62.527 66.667 0.00 0.00 46.71 5.25
1409 1572 5.588648 GGCTGCTTGATTGGTACAGTATTAA 59.411 40.000 0.00 0.00 42.39 1.40
1411 1574 6.538742 GCTGCTTGATTGGTACAGTATTAAGA 59.461 38.462 0.00 0.00 42.39 2.10
1456 1621 1.013596 TGTGTTGTGTGTGCTACTGC 58.986 50.000 0.00 0.00 40.20 4.40
1489 1654 5.175127 TGTTTCTTTTTGTTCTTTCCTGCC 58.825 37.500 0.00 0.00 0.00 4.85
1504 1669 1.622811 CCTGCCTCAGAAGTTCAGAGT 59.377 52.381 20.19 0.00 32.44 3.24
1505 1670 2.353605 CCTGCCTCAGAAGTTCAGAGTC 60.354 54.545 20.19 11.09 32.44 3.36
1507 1672 1.066502 GCCTCAGAAGTTCAGAGTCCC 60.067 57.143 20.19 7.87 29.19 4.46
1608 1777 3.125146 CGTGGTCTGTGTGTGAATAATGG 59.875 47.826 0.00 0.00 0.00 3.16
1621 1790 5.295787 TGTGAATAATGGTATTTGGAGACGC 59.704 40.000 0.00 0.00 29.69 5.19
1622 1791 4.819630 TGAATAATGGTATTTGGAGACGCC 59.180 41.667 0.00 0.00 29.69 5.68
1740 1913 4.580167 ACTGCACACAACTTGATAACATGT 59.420 37.500 0.00 0.00 36.24 3.21
1786 1968 8.680001 CCTGATTATCATTGATCAAGTTCAACA 58.320 33.333 14.54 7.74 38.37 3.33
1830 2012 1.318576 AACTGAAAAGGGCTGTTCGG 58.681 50.000 0.00 0.00 36.40 4.30
1845 2096 3.120792 TGTTCGGAAAACAGAGAGTTCG 58.879 45.455 0.00 0.00 40.26 3.95
1846 2097 1.779569 TCGGAAAACAGAGAGTTCGC 58.220 50.000 0.00 0.00 40.26 4.70
1852 2103 5.622378 GGAAAACAGAGAGTTCGCATAAAG 58.378 41.667 0.00 0.00 40.26 1.85
1862 2113 4.290155 AGTTCGCATAAAGCACAAAGTTG 58.710 39.130 0.00 0.00 46.13 3.16
1881 2132 3.953874 TGCATCAAAGTCGTTCGAAAA 57.046 38.095 0.00 0.00 0.00 2.29
1897 2148 4.945246 TCGAAAACTGTCAACTCTAGCTT 58.055 39.130 0.00 0.00 0.00 3.74
1898 2149 5.357257 TCGAAAACTGTCAACTCTAGCTTT 58.643 37.500 0.00 0.00 0.00 3.51
1905 2156 9.944376 AAACTGTCAACTCTAGCTTTATTATCA 57.056 29.630 0.00 0.00 0.00 2.15
1937 2193 9.758651 AAATCCTGAAAAATGTACAAAACCTAC 57.241 29.630 0.00 0.00 0.00 3.18
1939 2195 6.543100 TCCTGAAAAATGTACAAAACCTACGT 59.457 34.615 0.00 0.00 0.00 3.57
1957 2213 7.328737 ACCTACGTACTATGCTCAAAGATTTT 58.671 34.615 0.00 0.00 0.00 1.82
2022 2287 0.477204 CATCATGGGCAGGACAGGAT 59.523 55.000 0.00 0.00 39.65 3.24
2048 2313 2.026822 CCCTAGCAAGGTCACATGTCTT 60.027 50.000 0.00 0.00 41.89 3.01
2119 2384 3.402628 AAGTGTAGCCGTGAGAACAAT 57.597 42.857 0.00 0.00 0.00 2.71
2123 2388 1.804151 GTAGCCGTGAGAACAATTGCA 59.196 47.619 5.05 0.00 0.00 4.08
2124 2389 0.593128 AGCCGTGAGAACAATTGCAC 59.407 50.000 5.05 4.65 0.00 4.57
2128 2393 3.044986 CCGTGAGAACAATTGCACAAAG 58.955 45.455 5.05 0.00 0.00 2.77
2129 2394 2.468777 CGTGAGAACAATTGCACAAAGC 59.531 45.455 5.05 0.00 45.96 3.51
2153 2418 2.213499 CTTGCCACTAACCCGATCATC 58.787 52.381 0.00 0.00 0.00 2.92
2198 2464 1.308998 ACTGGGTCGTGCTTCTTTTG 58.691 50.000 0.00 0.00 0.00 2.44
2204 2470 0.308684 TCGTGCTTCTTTTGCAGCTG 59.691 50.000 10.11 10.11 41.41 4.24
2210 2476 3.130869 TGCTTCTTTTGCAGCTGAAAAGA 59.869 39.130 29.83 29.83 44.10 2.52
2211 2477 3.488678 GCTTCTTTTGCAGCTGAAAAGAC 59.511 43.478 31.56 23.97 44.97 3.01
2221 2487 1.433534 CTGAAAAGACAGCTCGGGAC 58.566 55.000 0.00 0.00 0.00 4.46
2235 2501 3.961414 GGACGGGCCCAGGTTTCA 61.961 66.667 24.92 0.00 0.00 2.69
2236 2502 2.114411 GACGGGCCCAGGTTTCAA 59.886 61.111 24.92 0.00 0.00 2.69
2237 2503 1.304134 GACGGGCCCAGGTTTCAAT 60.304 57.895 24.92 0.00 0.00 2.57
2238 2504 0.034863 GACGGGCCCAGGTTTCAATA 60.035 55.000 24.92 0.00 0.00 1.90
2239 2505 0.629058 ACGGGCCCAGGTTTCAATAT 59.371 50.000 24.92 0.00 0.00 1.28
2243 2509 2.625617 GGGCCCAGGTTTCAATATTCCA 60.626 50.000 19.95 0.00 0.00 3.53
2254 2520 6.607198 GGTTTCAATATTCCAGATTTCCAGGA 59.393 38.462 0.00 0.00 0.00 3.86
2255 2521 7.288621 GGTTTCAATATTCCAGATTTCCAGGAT 59.711 37.037 0.00 0.00 0.00 3.24
2256 2522 8.355913 GTTTCAATATTCCAGATTTCCAGGATC 58.644 37.037 0.00 0.00 0.00 3.36
2257 2523 7.398289 TCAATATTCCAGATTTCCAGGATCT 57.602 36.000 0.00 0.00 34.26 2.75
2258 2524 7.456725 TCAATATTCCAGATTTCCAGGATCTC 58.543 38.462 0.00 0.00 31.66 2.75
2259 2525 4.720775 ATTCCAGATTTCCAGGATCTCC 57.279 45.455 0.00 0.00 31.66 3.71
2261 2527 3.740780 TCCAGATTTCCAGGATCTCCTT 58.259 45.455 0.00 0.00 46.09 3.36
2262 2528 4.114597 TCCAGATTTCCAGGATCTCCTTT 58.885 43.478 0.00 0.00 46.09 3.11
2263 2529 4.541714 TCCAGATTTCCAGGATCTCCTTTT 59.458 41.667 0.00 0.00 46.09 2.27
2264 2530 5.015603 TCCAGATTTCCAGGATCTCCTTTTT 59.984 40.000 0.00 0.00 46.09 1.94
2289 2555 2.943449 GGGAAGTCCTTCACGACTAG 57.057 55.000 9.12 0.00 42.35 2.57
2290 2556 1.135053 GGGAAGTCCTTCACGACTAGC 60.135 57.143 9.12 0.00 42.35 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.815740 ACATAACGGAAATACATCAGTGTCC 59.184 40.000 0.00 0.00 39.77 4.02
2 3 6.312918 GTGACATAACGGAAATACATCAGTGT 59.687 38.462 0.00 0.00 42.39 3.55
4 5 5.518847 CGTGACATAACGGAAATACATCAGT 59.481 40.000 0.00 0.00 39.89 3.41
5 6 5.962939 CGTGACATAACGGAAATACATCAG 58.037 41.667 0.00 0.00 39.89 2.90
6 7 5.959652 CGTGACATAACGGAAATACATCA 57.040 39.130 0.00 0.00 39.89 3.07
17 18 4.033587 CCTTTCCATTACCGTGACATAACG 59.966 45.833 0.00 0.00 43.20 3.18
18 19 4.334481 CCCTTTCCATTACCGTGACATAAC 59.666 45.833 0.00 0.00 0.00 1.89
19 20 4.519213 CCCTTTCCATTACCGTGACATAA 58.481 43.478 0.00 0.00 0.00 1.90
20 21 3.118186 CCCCTTTCCATTACCGTGACATA 60.118 47.826 0.00 0.00 0.00 2.29
21 22 2.356741 CCCCTTTCCATTACCGTGACAT 60.357 50.000 0.00 0.00 0.00 3.06
22 23 1.003812 CCCCTTTCCATTACCGTGACA 59.996 52.381 0.00 0.00 0.00 3.58
23 24 1.003928 ACCCCTTTCCATTACCGTGAC 59.996 52.381 0.00 0.00 0.00 3.67
24 25 1.364269 ACCCCTTTCCATTACCGTGA 58.636 50.000 0.00 0.00 0.00 4.35
25 26 2.209690 AACCCCTTTCCATTACCGTG 57.790 50.000 0.00 0.00 0.00 4.94
26 27 3.893521 CATAACCCCTTTCCATTACCGT 58.106 45.455 0.00 0.00 0.00 4.83
27 28 2.621526 GCATAACCCCTTTCCATTACCG 59.378 50.000 0.00 0.00 0.00 4.02
28 29 2.963101 GGCATAACCCCTTTCCATTACC 59.037 50.000 0.00 0.00 0.00 2.85
60 61 6.569780 ACATTTTTCACGCTAGGTTCTTTTT 58.430 32.000 0.00 0.00 0.00 1.94
61 62 6.144078 ACATTTTTCACGCTAGGTTCTTTT 57.856 33.333 0.00 0.00 0.00 2.27
62 63 5.767816 ACATTTTTCACGCTAGGTTCTTT 57.232 34.783 0.00 0.00 0.00 2.52
63 64 5.560183 CGAACATTTTTCACGCTAGGTTCTT 60.560 40.000 0.00 0.00 33.19 2.52
64 65 4.084013 CGAACATTTTTCACGCTAGGTTCT 60.084 41.667 0.00 0.00 33.19 3.01
65 66 4.084223 TCGAACATTTTTCACGCTAGGTTC 60.084 41.667 0.00 0.00 0.00 3.62
66 67 3.810941 TCGAACATTTTTCACGCTAGGTT 59.189 39.130 0.00 0.00 0.00 3.50
67 68 3.395639 TCGAACATTTTTCACGCTAGGT 58.604 40.909 0.00 0.00 0.00 3.08
68 69 4.600012 ATCGAACATTTTTCACGCTAGG 57.400 40.909 0.00 0.00 0.00 3.02
69 70 5.851177 ACAAATCGAACATTTTTCACGCTAG 59.149 36.000 0.00 0.00 0.00 3.42
70 71 5.753744 ACAAATCGAACATTTTTCACGCTA 58.246 33.333 0.00 0.00 0.00 4.26
71 72 4.606961 ACAAATCGAACATTTTTCACGCT 58.393 34.783 0.00 0.00 0.00 5.07
72 73 4.439449 TGACAAATCGAACATTTTTCACGC 59.561 37.500 0.00 0.00 0.00 5.34
73 74 6.507361 CATGACAAATCGAACATTTTTCACG 58.493 36.000 1.96 0.00 32.63 4.35
74 75 6.291385 GCATGACAAATCGAACATTTTTCAC 58.709 36.000 0.00 0.00 32.63 3.18
75 76 5.404968 GGCATGACAAATCGAACATTTTTCA 59.595 36.000 0.00 2.33 33.82 2.69
76 77 5.634859 AGGCATGACAAATCGAACATTTTTC 59.365 36.000 0.00 0.00 0.00 2.29
82 83 5.697473 TTTTAGGCATGACAAATCGAACA 57.303 34.783 0.00 0.00 0.00 3.18
84 85 7.028962 CAGAATTTTAGGCATGACAAATCGAA 58.971 34.615 0.00 0.00 0.00 3.71
96 97 6.003326 TCAGTGAATGTCAGAATTTTAGGCA 58.997 36.000 0.00 0.00 0.00 4.75
156 157 1.948104 TTCAAGCGTGCACTAGTTGT 58.052 45.000 16.19 0.00 0.00 3.32
175 176 1.597937 CGCGCTGCAAGACTTCTTTTT 60.598 47.619 5.56 0.00 34.07 1.94
176 177 0.040958 CGCGCTGCAAGACTTCTTTT 60.041 50.000 5.56 0.00 34.07 2.27
177 178 0.880278 TCGCGCTGCAAGACTTCTTT 60.880 50.000 5.56 0.00 34.07 2.52
178 179 0.671781 ATCGCGCTGCAAGACTTCTT 60.672 50.000 5.56 0.00 34.07 2.52
179 180 1.079543 ATCGCGCTGCAAGACTTCT 60.080 52.632 5.56 0.00 34.07 2.85
180 181 1.059994 CATCGCGCTGCAAGACTTC 59.940 57.895 5.56 0.00 34.07 3.01
181 182 2.393768 CCATCGCGCTGCAAGACTT 61.394 57.895 5.56 0.00 34.07 3.01
182 183 2.816958 CCATCGCGCTGCAAGACT 60.817 61.111 5.56 0.00 34.07 3.24
282 294 0.937304 CGCCATATGTACCAGTGTGC 59.063 55.000 1.24 0.00 0.00 4.57
283 295 1.134521 ACCGCCATATGTACCAGTGTG 60.135 52.381 1.24 0.00 0.00 3.82
284 296 1.200519 ACCGCCATATGTACCAGTGT 58.799 50.000 1.24 0.00 0.00 3.55
285 297 3.006430 TGATACCGCCATATGTACCAGTG 59.994 47.826 1.24 0.00 0.00 3.66
311 323 1.001706 TCGATACTTTCAGCGGATCGG 60.002 52.381 6.90 0.00 39.79 4.18
313 325 3.046390 CAGTCGATACTTTCAGCGGATC 58.954 50.000 0.00 0.00 31.97 3.36
314 326 2.688446 TCAGTCGATACTTTCAGCGGAT 59.312 45.455 0.00 0.00 31.97 4.18
500 553 3.610040 ATAGTGTTGAACTCATGCGGA 57.390 42.857 0.00 0.00 40.56 5.54
543 642 2.821546 TCCAGATAGCAAAACGGATCG 58.178 47.619 0.00 0.00 0.00 3.69
572 676 0.179134 GTTGTGTCCGATCGCTAGCT 60.179 55.000 13.93 0.00 0.00 3.32
585 689 3.078097 TGTAGTGTTGCTTGTGTTGTGT 58.922 40.909 0.00 0.00 0.00 3.72
586 690 3.755965 TGTAGTGTTGCTTGTGTTGTG 57.244 42.857 0.00 0.00 0.00 3.33
587 691 3.504134 TGTTGTAGTGTTGCTTGTGTTGT 59.496 39.130 0.00 0.00 0.00 3.32
588 692 4.090138 TGTTGTAGTGTTGCTTGTGTTG 57.910 40.909 0.00 0.00 0.00 3.33
589 693 3.756434 ACTGTTGTAGTGTTGCTTGTGTT 59.244 39.130 0.00 0.00 38.49 3.32
590 694 3.343617 ACTGTTGTAGTGTTGCTTGTGT 58.656 40.909 0.00 0.00 38.49 3.72
651 763 2.811431 CCTTTGACTTCAACGGCACATA 59.189 45.455 1.85 0.00 38.23 2.29
652 764 1.608590 CCTTTGACTTCAACGGCACAT 59.391 47.619 1.85 0.00 38.23 3.21
653 765 1.021202 CCTTTGACTTCAACGGCACA 58.979 50.000 1.85 0.00 38.23 4.57
719 832 2.546899 ACATTGGTAGCCTGGTGACTA 58.453 47.619 0.00 0.00 0.00 2.59
732 845 1.537202 GCTTGCTCGAAGAACATTGGT 59.463 47.619 0.00 0.00 30.48 3.67
773 886 0.819259 TGCTTTTTCGACAGGCTGCT 60.819 50.000 15.89 1.32 0.00 4.24
776 889 1.952263 GCTGCTTTTTCGACAGGCT 59.048 52.632 2.60 0.00 31.94 4.58
860 973 1.003118 TCATGCTTTTACGGGCACTCT 59.997 47.619 0.00 0.00 41.39 3.24
871 984 3.983344 GCGATGACAAAGTTCATGCTTTT 59.017 39.130 0.00 0.00 36.30 2.27
880 993 2.198827 TCCATGGCGATGACAAAGTT 57.801 45.000 10.66 0.00 0.00 2.66
882 995 3.124128 CGATATCCATGGCGATGACAAAG 59.876 47.826 10.66 0.00 0.00 2.77
883 996 3.066380 CGATATCCATGGCGATGACAAA 58.934 45.455 10.66 0.00 0.00 2.83
884 997 2.612721 CCGATATCCATGGCGATGACAA 60.613 50.000 10.66 0.00 0.00 3.18
885 998 1.066929 CCGATATCCATGGCGATGACA 60.067 52.381 10.66 0.00 0.00 3.58
886 999 1.645034 CCGATATCCATGGCGATGAC 58.355 55.000 10.66 0.00 0.00 3.06
887 1000 0.536724 CCCGATATCCATGGCGATGA 59.463 55.000 10.66 0.00 0.00 2.92
888 1001 0.250234 ACCCGATATCCATGGCGATG 59.750 55.000 6.96 1.01 0.00 3.84
889 1002 1.860641 TACCCGATATCCATGGCGAT 58.139 50.000 6.96 1.88 0.00 4.58
901 1016 4.174704 TGCCCGTCTATATATACCCGAT 57.825 45.455 7.53 0.00 0.00 4.18
979 1094 5.049818 CCATCTTCCTCGATCTTTTGTATGC 60.050 44.000 0.00 0.00 0.00 3.14
983 1098 3.274288 GCCATCTTCCTCGATCTTTTGT 58.726 45.455 0.00 0.00 0.00 2.83
984 1099 2.286294 CGCCATCTTCCTCGATCTTTTG 59.714 50.000 0.00 0.00 0.00 2.44
985 1100 2.093447 ACGCCATCTTCCTCGATCTTTT 60.093 45.455 0.00 0.00 0.00 2.27
998 1133 0.810031 GTACCGCATGAACGCCATCT 60.810 55.000 0.00 0.00 31.94 2.90
1301 1436 3.582208 AGAGATTATTGGGAGGCTGCTAG 59.418 47.826 5.84 0.00 0.00 3.42
1350 1501 1.475280 CCAAGCCAGCTAGTACGTACA 59.525 52.381 26.55 12.17 0.00 2.90
1351 1502 1.747355 TCCAAGCCAGCTAGTACGTAC 59.253 52.381 18.10 18.10 0.00 3.67
1352 1503 2.133281 TCCAAGCCAGCTAGTACGTA 57.867 50.000 0.00 0.00 0.00 3.57
1353 1504 1.137086 CATCCAAGCCAGCTAGTACGT 59.863 52.381 0.00 0.00 0.00 3.57
1354 1505 1.858091 CATCCAAGCCAGCTAGTACG 58.142 55.000 0.00 0.00 0.00 3.67
1355 1506 1.587547 GCATCCAAGCCAGCTAGTAC 58.412 55.000 0.00 0.00 0.00 2.73
1456 1621 3.954258 ACAAAAAGAAACAGGTCCAGAGG 59.046 43.478 0.00 0.00 0.00 3.69
1489 1654 2.233431 CAGGGGACTCTGAACTTCTGAG 59.767 54.545 19.12 19.12 44.75 3.35
1504 1669 2.892852 CAGCTGTTCATTTTTCAGGGGA 59.107 45.455 5.25 0.00 0.00 4.81
1505 1670 2.892852 TCAGCTGTTCATTTTTCAGGGG 59.107 45.455 14.67 0.00 0.00 4.79
1507 1672 4.301628 GGTTCAGCTGTTCATTTTTCAGG 58.698 43.478 14.67 0.00 0.00 3.86
1608 1777 1.143969 CGGACGGCGTCTCCAAATAC 61.144 60.000 35.42 17.58 32.47 1.89
1621 1790 2.752322 TAGCAACAACGGTCGGACGG 62.752 60.000 13.41 13.41 38.39 4.79
1622 1791 1.372004 TAGCAACAACGGTCGGACG 60.372 57.895 1.43 0.46 40.31 4.79
1631 1800 3.844943 GCAGAGAACAACGTAGCAACAAC 60.845 47.826 0.00 0.00 0.00 3.32
1632 1801 2.286833 GCAGAGAACAACGTAGCAACAA 59.713 45.455 0.00 0.00 0.00 2.83
1633 1802 1.864711 GCAGAGAACAACGTAGCAACA 59.135 47.619 0.00 0.00 0.00 3.33
1677 1846 2.734079 GTGCAGCGATTAGGAGCTATTC 59.266 50.000 0.00 0.00 42.52 1.75
1680 1849 1.067669 CTGTGCAGCGATTAGGAGCTA 59.932 52.381 0.00 0.00 42.52 3.32
1717 1890 4.580167 ACATGTTATCAAGTTGTGTGCAGT 59.420 37.500 2.11 0.00 0.00 4.40
1749 1931 4.137116 TGATAATCAGGTCGTTCCCTTG 57.863 45.455 0.00 0.00 36.75 3.61
1756 1938 6.586344 ACTTGATCAATGATAATCAGGTCGT 58.414 36.000 8.96 0.00 37.59 4.34
1806 1988 4.363138 GAACAGCCCTTTTCAGTTTCTTG 58.637 43.478 0.00 0.00 0.00 3.02
1809 1991 2.287608 CCGAACAGCCCTTTTCAGTTTC 60.288 50.000 0.00 0.00 0.00 2.78
1810 1992 1.681264 CCGAACAGCCCTTTTCAGTTT 59.319 47.619 0.00 0.00 0.00 2.66
1820 2002 0.875059 CTCTGTTTTCCGAACAGCCC 59.125 55.000 12.72 0.00 45.34 5.19
1830 2012 5.082723 GCTTTATGCGAACTCTCTGTTTTC 58.917 41.667 0.00 0.00 39.30 2.29
1845 2096 3.989167 TGATGCAACTTTGTGCTTTATGC 59.011 39.130 0.00 0.00 45.17 3.14
1846 2097 6.201425 ACTTTGATGCAACTTTGTGCTTTATG 59.799 34.615 0.00 0.00 45.17 1.90
1852 2103 2.468777 CGACTTTGATGCAACTTTGTGC 59.531 45.455 0.00 0.00 45.15 4.57
1862 2113 3.659444 CAGTTTTCGAACGACTTTGATGC 59.341 43.478 9.93 0.00 0.00 3.91
1881 2132 9.944376 TTTGATAATAAAGCTAGAGTTGACAGT 57.056 29.630 0.00 0.00 0.00 3.55
1937 2193 9.907576 CTCTTTAAAATCTTTGAGCATAGTACG 57.092 33.333 0.00 0.00 0.00 3.67
2022 2287 1.159905 TGACCTTGCTAGGGGTGGA 59.840 57.895 18.75 0.00 46.58 4.02
2097 2362 4.325028 TTGTTCTCACGGCTACACTTTA 57.675 40.909 0.00 0.00 0.00 1.85
2099 2364 2.902705 TTGTTCTCACGGCTACACTT 57.097 45.000 0.00 0.00 0.00 3.16
2129 2394 2.684001 TCGGGTTAGTGGCAAGTATG 57.316 50.000 0.00 0.00 0.00 2.39
2176 2442 2.052782 AAGAAGCACGACCCAGTTTT 57.947 45.000 0.00 0.00 0.00 2.43
2181 2447 0.749818 TGCAAAAGAAGCACGACCCA 60.750 50.000 0.00 0.00 37.02 4.51
2182 2448 0.040067 CTGCAAAAGAAGCACGACCC 60.040 55.000 0.00 0.00 37.02 4.46
2185 2451 0.308684 CAGCTGCAAAAGAAGCACGA 59.691 50.000 0.00 0.00 42.06 4.35
2204 2470 1.014564 CCGTCCCGAGCTGTCTTTTC 61.015 60.000 0.00 0.00 0.00 2.29
2219 2485 0.034863 TATTGAAACCTGGGCCCGTC 60.035 55.000 19.37 9.71 0.00 4.79
2221 2487 1.681264 GAATATTGAAACCTGGGCCCG 59.319 52.381 19.37 12.19 0.00 6.13
2224 2490 3.631250 TCTGGAATATTGAAACCTGGGC 58.369 45.455 0.00 0.00 0.00 5.36
2225 2491 6.183360 GGAAATCTGGAATATTGAAACCTGGG 60.183 42.308 0.00 0.00 0.00 4.45
2227 2493 7.408756 TGGAAATCTGGAATATTGAAACCTG 57.591 36.000 0.00 0.00 0.00 4.00
2228 2494 6.608808 CCTGGAAATCTGGAATATTGAAACCT 59.391 38.462 0.00 0.00 36.68 3.50
2230 2496 7.645058 TCCTGGAAATCTGGAATATTGAAAC 57.355 36.000 0.00 0.00 40.01 2.78
2233 2499 7.398289 AGATCCTGGAAATCTGGAATATTGA 57.602 36.000 0.00 0.00 44.87 2.57
2234 2500 6.658391 GGAGATCCTGGAAATCTGGAATATTG 59.342 42.308 0.00 0.00 44.87 1.90
2235 2501 6.565703 AGGAGATCCTGGAAATCTGGAATATT 59.434 38.462 0.00 0.00 46.55 1.28
2236 2502 6.097062 AGGAGATCCTGGAAATCTGGAATAT 58.903 40.000 0.00 0.00 46.55 1.28
2237 2503 5.480710 AGGAGATCCTGGAAATCTGGAATA 58.519 41.667 0.00 0.00 46.55 1.75
2238 2504 4.314238 AGGAGATCCTGGAAATCTGGAAT 58.686 43.478 0.00 0.00 46.55 3.01
2239 2505 3.740780 AGGAGATCCTGGAAATCTGGAA 58.259 45.455 0.00 0.00 46.55 3.53
2267 2533 0.388263 GTCGTGAAGGACTTCCCGTC 60.388 60.000 14.68 7.43 40.44 4.79
2268 2534 0.826672 AGTCGTGAAGGACTTCCCGT 60.827 55.000 14.68 0.00 44.65 5.28
2269 2535 1.132643 CTAGTCGTGAAGGACTTCCCG 59.867 57.143 10.62 10.07 44.65 5.14
2270 2536 1.135053 GCTAGTCGTGAAGGACTTCCC 60.135 57.143 10.62 0.00 44.65 3.97
2271 2537 2.281140 GCTAGTCGTGAAGGACTTCC 57.719 55.000 10.62 0.00 44.65 3.46


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

AutoCloner maintained by Alex Coulton.