Multiple sequence alignment - TraesCS2B01G412500

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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 TraesCS2B01G412500 chr2B 100.000 2468 0 0 1 2468 587246700 587249167 0.000000e+00 4558.0
1 TraesCS2B01G412500 chr2B 85.000 80 9 3 251 329 652277998 652277921 7.320000e-11 78.7
2 TraesCS2B01G412500 chr2A 88.783 1471 135 14 719 2166 644253569 644255032 0.000000e+00 1775.0
3 TraesCS2B01G412500 chr2A 90.220 726 54 4 4 712 644252451 644253176 0.000000e+00 931.0
4 TraesCS2B01G412500 chr2A 87.879 99 12 0 2180 2278 644255262 644255360 1.550000e-22 117.0
5 TraesCS2B01G412500 chr2D 89.617 1435 68 32 367 1768 499731871 499733257 0.000000e+00 1749.0
6 TraesCS2B01G412500 chr2D 90.211 521 45 4 1760 2278 499734928 499735444 0.000000e+00 675.0
7 TraesCS2B01G412500 chr3B 87.778 90 10 1 1690 1779 813907100 813907012 1.210000e-18 104.0
8 TraesCS2B01G412500 chr1B 76.440 191 29 11 141 324 567980587 567980406 3.380000e-14 89.8
9 TraesCS2B01G412500 chr4D 81.818 110 14 3 1859 1962 306460424 306460315 1.220000e-13 87.9
10 TraesCS2B01G412500 chr4D 83.117 77 8 5 1690 1763 51844909 51844983 5.700000e-07 65.8
11 TraesCS2B01G412500 chr6A 74.429 219 39 13 122 333 554782065 554782273 7.320000e-11 78.7
12 TraesCS2B01G412500 chr3A 84.146 82 7 6 251 328 552020606 552020527 9.470000e-10 75.0
13 TraesCS2B01G412500 chr6D 83.750 80 9 4 1690 1766 389598671 389598749 3.400000e-09 73.1
14 TraesCS2B01G412500 chr6D 81.250 80 14 1 251 329 34189716 34189637 2.050000e-06 63.9
15 TraesCS2B01G412500 chr1A 84.416 77 9 3 255 329 519631384 519631309 3.400000e-09 73.1
16 TraesCS2B01G412500 chr7D 85.507 69 9 1 1859 1926 398001106 398001174 1.220000e-08 71.3
17 TraesCS2B01G412500 chr7D 82.558 86 8 6 248 331 554369281 554369361 4.400000e-08 69.4
18 TraesCS2B01G412500 chr7D 80.899 89 11 5 1934 2019 203360000 203359915 5.700000e-07 65.8
19 TraesCS2B01G412500 chr7D 90.476 42 4 0 1676 1717 420412726 420412767 3.430000e-04 56.5
20 TraesCS2B01G412500 chr7D 89.130 46 4 1 73 117 621777498 621777453 3.430000e-04 56.5
21 TraesCS2B01G412500 chr7B 90.566 53 2 3 251 301 685662308 685662257 1.580000e-07 67.6
22 TraesCS2B01G412500 chr7B 78.431 102 14 7 1690 1785 477411945 477411846 2.650000e-05 60.2
23 TraesCS2B01G412500 chr1D 83.871 62 7 3 1690 1748 377965444 377965505 3.430000e-04 56.5


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 TraesCS2B01G412500 chr2B 587246700 587249167 2467 False 4558 4558 100.000000 1 2468 1 chr2B.!!$F1 2467
1 TraesCS2B01G412500 chr2A 644252451 644255360 2909 False 941 1775 88.960667 4 2278 3 chr2A.!!$F1 2274
2 TraesCS2B01G412500 chr2D 499731871 499735444 3573 False 1212 1749 89.914000 367 2278 2 chr2D.!!$F1 1911

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
69 70 0.240145 GGCGAACTTTGGTGTTAGGC 59.76 55.0 0.0 0.0 39.75 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 3973 0.029035 CGGTTCACGGATCTCTACGG 59.971 60.0 0.0 0.0 39.42 4.02 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
37 38 1.787155 CGAGGTTATGATTTCTCGGCG 59.213 52.381 0.00 0.00 43.49 6.46
52 53 4.666532 GCGTGCACACAAGACGGC 62.667 66.667 18.64 5.45 33.68 5.68
55 56 2.202946 TGCACACAAGACGGCGAA 60.203 55.556 16.62 0.00 0.00 4.70
67 68 1.193874 GACGGCGAACTTTGGTGTTAG 59.806 52.381 16.62 0.00 0.00 2.34
68 69 0.515564 CGGCGAACTTTGGTGTTAGG 59.484 55.000 0.00 0.00 0.00 2.69
69 70 0.240145 GGCGAACTTTGGTGTTAGGC 59.760 55.000 0.00 0.00 39.75 3.93
79 80 2.695359 TGGTGTTAGGCGTTTCAGATC 58.305 47.619 0.00 0.00 0.00 2.75
95 96 5.964958 TCAGATCAATTCAAGGGTTCAAC 57.035 39.130 0.00 0.00 0.00 3.18
104 105 2.635915 TCAAGGGTTCAACGGTGACTAT 59.364 45.455 0.44 0.00 31.90 2.12
107 108 1.467342 GGGTTCAACGGTGACTATTGC 59.533 52.381 0.44 0.00 31.90 3.56
135 143 1.792367 GGGCGTTGCACAAAGAATTTC 59.208 47.619 0.31 0.00 35.03 2.17
136 144 1.792367 GGCGTTGCACAAAGAATTTCC 59.208 47.619 0.31 0.00 35.03 3.13
137 145 2.468831 GCGTTGCACAAAGAATTTCCA 58.531 42.857 0.31 0.00 35.03 3.53
140 148 4.024977 GCGTTGCACAAAGAATTTCCAAAT 60.025 37.500 0.31 0.00 35.03 2.32
147 155 6.424509 GCACAAAGAATTTCCAAATGTCATCA 59.575 34.615 0.00 0.00 35.03 3.07
155 163 2.562298 TCCAAATGTCATCAACAAGGCC 59.438 45.455 0.00 0.00 42.37 5.19
187 205 2.504244 GAGGAGCGACGACAACGG 60.504 66.667 0.00 0.00 44.46 4.44
188 206 4.719369 AGGAGCGACGACAACGGC 62.719 66.667 0.00 0.00 45.02 5.68
194 212 4.117372 GACGACAACGGCGCTTCG 62.117 66.667 19.64 19.64 44.46 3.79
195 213 4.634133 ACGACAACGGCGCTTCGA 62.634 61.111 25.63 0.00 44.46 3.71
205 223 1.729838 GCGCTTCGACGACTCACTT 60.730 57.895 0.00 0.00 34.06 3.16
213 231 2.287644 TCGACGACTCACTTTGACGTTA 59.712 45.455 0.00 0.00 36.18 3.18
221 239 2.358582 TCACTTTGACGTTAGTGGTCGA 59.641 45.455 19.62 4.79 41.58 4.20
233 251 1.012486 GTGGTCGATCGGTGGTTCAC 61.012 60.000 16.41 10.63 0.00 3.18
235 253 0.320073 GGTCGATCGGTGGTTCACAA 60.320 55.000 16.41 0.00 35.86 3.33
307 325 9.481340 CTTCTCATGAACTTTATAATCCATCGA 57.519 33.333 0.00 0.00 0.00 3.59
367 385 2.294074 CTTTCCAAGGTCGTGAAACCA 58.706 47.619 0.00 0.00 42.12 3.67
407 425 8.302515 AGCTTAGATCATGATCCAAAATGTTT 57.697 30.769 28.23 11.82 38.58 2.83
491 509 3.181469 ACAAACACGAAGCTCCTAGAACA 60.181 43.478 0.00 0.00 0.00 3.18
627 652 2.440247 CCCACCCTCCAAATCCGC 60.440 66.667 0.00 0.00 0.00 5.54
720 745 2.438434 CACTCCACGCAATCCCCC 60.438 66.667 0.00 0.00 0.00 5.40
860 1271 4.933064 CGGCGGGATCTGCGAGAC 62.933 72.222 0.00 0.00 0.00 3.36
879 1290 4.215908 AGACTATCCAATTAGCTCCGTCA 58.784 43.478 0.00 0.00 0.00 4.35
919 1330 3.560278 CGCCGTGTATGCCGTTCC 61.560 66.667 0.00 0.00 0.00 3.62
981 1392 3.093717 TCGAGTTCTTGAAGACACACC 57.906 47.619 0.00 0.00 0.00 4.16
982 1393 2.429250 TCGAGTTCTTGAAGACACACCA 59.571 45.455 0.00 0.00 0.00 4.17
1005 1433 3.594603 ATTCGCTAGAATACGATGGGG 57.405 47.619 0.00 0.00 44.65 4.96
1068 1496 1.450312 CGTGGAGATGAAGGTGCCC 60.450 63.158 0.00 0.00 0.00 5.36
1160 1590 5.424252 TCATAGGACATTTCTACGGGAAACT 59.576 40.000 7.74 4.43 45.29 2.66
1200 1630 0.890542 GAGGCGGCCATGCATGAATA 60.891 55.000 28.31 0.00 36.28 1.75
1499 1932 0.785708 GCGAGCGTGATGTTTTGTCG 60.786 55.000 0.00 0.00 0.00 4.35
1502 1935 3.156401 GCGTGATGTTTTGTCGCAA 57.844 47.368 0.00 0.00 45.01 4.85
1561 2001 0.255890 GGAATGGCCAGGAGTTGCTA 59.744 55.000 13.05 0.00 36.34 3.49
1630 2070 5.360714 TGCTCTGTTCTTGTCTTTTGGAATT 59.639 36.000 0.00 0.00 0.00 2.17
1640 2080 4.344679 TGTCTTTTGGAATTGGCAGATTGT 59.655 37.500 0.00 0.00 0.00 2.71
1643 2083 3.574284 TTGGAATTGGCAGATTGTTCG 57.426 42.857 0.00 0.00 0.00 3.95
1665 2105 2.507339 AATCTGTTGGTTGGCAAACG 57.493 45.000 11.20 0.00 37.15 3.60
1680 2120 3.004024 CAAACGCTTGCAATGAAGTCT 57.996 42.857 0.00 0.00 0.00 3.24
1682 2122 4.536065 CAAACGCTTGCAATGAAGTCTAA 58.464 39.130 0.00 0.00 0.00 2.10
1683 2123 3.813529 ACGCTTGCAATGAAGTCTAAC 57.186 42.857 0.00 0.00 0.00 2.34
1684 2124 3.138304 ACGCTTGCAATGAAGTCTAACA 58.862 40.909 0.00 0.00 0.00 2.41
1686 2126 4.093514 CGCTTGCAATGAAGTCTAACATG 58.906 43.478 0.00 0.00 0.00 3.21
1705 2145 6.884280 ACATGGATTTTCGAGAAAACTTCT 57.116 33.333 12.51 0.00 42.32 2.85
1706 2146 6.672147 ACATGGATTTTCGAGAAAACTTCTG 58.328 36.000 12.51 10.58 42.32 3.02
1719 2159 8.538856 CGAGAAAACTTCTGATCTATTCATCAC 58.461 37.037 0.00 0.00 40.87 3.06
1734 2174 4.871933 TCATCACGTCATGGCAGTATAT 57.128 40.909 0.00 0.00 0.00 0.86
1779 3898 9.818270 AAAATTACATCCATGTCCATAGATCAT 57.182 29.630 0.00 0.00 41.97 2.45
1859 3986 8.627208 TTAAATTAGTATCCGTAGAGATCCGT 57.373 34.615 0.00 0.00 0.00 4.69
1864 3991 1.386533 TCCGTAGAGATCCGTGAACC 58.613 55.000 0.00 0.00 0.00 3.62
1899 4026 5.473162 CAGATGATTAGGTTTGTTGTGGTGA 59.527 40.000 0.00 0.00 0.00 4.02
1912 4039 2.739943 TGTGGTGAAATCAACCCACAA 58.260 42.857 18.36 7.10 44.71 3.33
1932 4059 5.991606 CACAAAGTTCAAGTCCTAGACATCA 59.008 40.000 0.00 0.00 34.60 3.07
1946 4073 4.361451 AGACATCAATGGTCGCATTTTC 57.639 40.909 0.00 0.00 40.20 2.29
1987 4114 5.000591 ACATTGACGGTGTATGTTCAATGA 58.999 37.500 23.25 0.00 43.93 2.57
2032 4159 0.537143 AGGCGTTCATGGCAACTTCA 60.537 50.000 0.00 0.00 36.77 3.02
2156 4285 3.296516 GCATCTGCGTTTGTAGTGC 57.703 52.632 0.00 0.00 31.84 4.40
2278 4623 4.434713 ACCGCTGGATATTGAAAACAAC 57.565 40.909 1.50 0.00 0.00 3.32
2279 4624 4.079253 ACCGCTGGATATTGAAAACAACT 58.921 39.130 1.50 0.00 0.00 3.16
2280 4625 5.250200 ACCGCTGGATATTGAAAACAACTA 58.750 37.500 1.50 0.00 0.00 2.24
2281 4626 5.885912 ACCGCTGGATATTGAAAACAACTAT 59.114 36.000 1.50 0.00 0.00 2.12
2282 4627 6.377146 ACCGCTGGATATTGAAAACAACTATT 59.623 34.615 1.50 0.00 0.00 1.73
2283 4628 6.692681 CCGCTGGATATTGAAAACAACTATTG 59.307 38.462 0.00 0.00 0.00 1.90
2284 4629 7.415095 CCGCTGGATATTGAAAACAACTATTGA 60.415 37.037 0.00 0.00 0.00 2.57
2285 4630 8.131100 CGCTGGATATTGAAAACAACTATTGAT 58.869 33.333 0.00 0.00 0.00 2.57
2286 4631 9.807649 GCTGGATATTGAAAACAACTATTGATT 57.192 29.630 0.00 0.00 0.00 2.57
2293 4638 6.446318 TGAAAACAACTATTGATTGAGGTGC 58.554 36.000 0.00 0.00 33.42 5.01
2294 4639 5.391312 AAACAACTATTGATTGAGGTGCC 57.609 39.130 0.00 0.00 33.42 5.01
2295 4640 4.032960 ACAACTATTGATTGAGGTGCCA 57.967 40.909 0.00 0.00 33.42 4.92
2296 4641 3.758554 ACAACTATTGATTGAGGTGCCAC 59.241 43.478 0.00 0.00 33.42 5.01
2297 4642 3.004752 ACTATTGATTGAGGTGCCACC 57.995 47.619 5.50 5.50 38.99 4.61
2298 4643 2.301346 CTATTGATTGAGGTGCCACCC 58.699 52.381 11.06 2.62 39.75 4.61
2299 4644 0.680921 ATTGATTGAGGTGCCACCCG 60.681 55.000 11.06 0.00 39.75 5.28
2300 4645 2.438434 GATTGAGGTGCCACCCGG 60.438 66.667 11.06 0.00 39.75 5.73
2301 4646 3.256960 ATTGAGGTGCCACCCGGT 61.257 61.111 11.06 0.00 39.75 5.28
2302 4647 3.567579 ATTGAGGTGCCACCCGGTG 62.568 63.158 11.06 10.95 39.75 4.94
2313 4658 4.973055 CCCGGTGGCGTCGTTTGA 62.973 66.667 0.00 0.00 0.00 2.69
2314 4659 3.411351 CCGGTGGCGTCGTTTGAG 61.411 66.667 0.00 0.00 0.00 3.02
2315 4660 2.355363 CGGTGGCGTCGTTTGAGA 60.355 61.111 0.00 0.00 0.00 3.27
2316 4661 2.372690 CGGTGGCGTCGTTTGAGAG 61.373 63.158 0.00 0.00 0.00 3.20
2317 4662 2.027625 GGTGGCGTCGTTTGAGAGG 61.028 63.158 0.00 0.00 0.00 3.69
2318 4663 1.006571 GTGGCGTCGTTTGAGAGGA 60.007 57.895 0.00 0.00 0.00 3.71
2319 4664 0.599204 GTGGCGTCGTTTGAGAGGAA 60.599 55.000 0.00 0.00 0.00 3.36
2320 4665 0.599204 TGGCGTCGTTTGAGAGGAAC 60.599 55.000 0.00 0.00 0.00 3.62
2321 4666 0.599204 GGCGTCGTTTGAGAGGAACA 60.599 55.000 0.00 0.00 0.00 3.18
2322 4667 1.429463 GCGTCGTTTGAGAGGAACAT 58.571 50.000 0.00 0.00 0.00 2.71
2323 4668 1.126846 GCGTCGTTTGAGAGGAACATG 59.873 52.381 0.00 0.00 0.00 3.21
2324 4669 1.126846 CGTCGTTTGAGAGGAACATGC 59.873 52.381 0.00 0.00 0.00 4.06
2325 4670 1.126846 GTCGTTTGAGAGGAACATGCG 59.873 52.381 0.00 0.00 0.00 4.73
2326 4671 0.179215 CGTTTGAGAGGAACATGCGC 60.179 55.000 0.00 0.00 0.00 6.09
2327 4672 0.179215 GTTTGAGAGGAACATGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
2328 4673 1.911293 TTTGAGAGGAACATGCGCGC 61.911 55.000 27.26 27.26 0.00 6.86
2329 4674 2.815211 GAGAGGAACATGCGCGCA 60.815 61.111 38.27 38.27 0.00 6.09
2330 4675 3.088500 GAGAGGAACATGCGCGCAC 62.089 63.158 39.05 23.74 0.00 5.34
2331 4676 4.505217 GAGGAACATGCGCGCACG 62.505 66.667 39.05 33.03 44.07 5.34
2333 4678 4.383602 GGAACATGCGCGCACGTT 62.384 61.111 40.96 40.96 42.83 3.99
2334 4679 2.426752 GAACATGCGCGCACGTTT 60.427 55.556 40.42 30.00 42.83 3.60
2335 4680 2.417553 GAACATGCGCGCACGTTTC 61.418 57.895 40.42 32.41 42.83 2.78
2336 4681 3.872409 AACATGCGCGCACGTTTCC 62.872 57.895 36.40 4.27 42.83 3.13
2395 4740 9.696917 AAAAACATCTAAACAATCCTCACATTC 57.303 29.630 0.00 0.00 0.00 2.67
2396 4741 8.408043 AAACATCTAAACAATCCTCACATTCA 57.592 30.769 0.00 0.00 0.00 2.57
2397 4742 8.585471 AACATCTAAACAATCCTCACATTCAT 57.415 30.769 0.00 0.00 0.00 2.57
2398 4743 8.218338 ACATCTAAACAATCCTCACATTCATC 57.782 34.615 0.00 0.00 0.00 2.92
2399 4744 8.051535 ACATCTAAACAATCCTCACATTCATCT 58.948 33.333 0.00 0.00 0.00 2.90
2400 4745 9.551734 CATCTAAACAATCCTCACATTCATCTA 57.448 33.333 0.00 0.00 0.00 1.98
2402 4747 9.958180 TCTAAACAATCCTCACATTCATCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
2433 4778 4.965119 AAAAATTACCATCGCTCCTCAC 57.035 40.909 0.00 0.00 0.00 3.51
2434 4779 2.622064 AATTACCATCGCTCCTCACC 57.378 50.000 0.00 0.00 0.00 4.02
2435 4780 1.794714 ATTACCATCGCTCCTCACCT 58.205 50.000 0.00 0.00 0.00 4.00
2436 4781 1.568504 TTACCATCGCTCCTCACCTT 58.431 50.000 0.00 0.00 0.00 3.50
2437 4782 1.112113 TACCATCGCTCCTCACCTTC 58.888 55.000 0.00 0.00 0.00 3.46
2438 4783 0.904865 ACCATCGCTCCTCACCTTCA 60.905 55.000 0.00 0.00 0.00 3.02
2439 4784 0.467384 CCATCGCTCCTCACCTTCAT 59.533 55.000 0.00 0.00 0.00 2.57
2440 4785 1.539929 CCATCGCTCCTCACCTTCATC 60.540 57.143 0.00 0.00 0.00 2.92
2441 4786 1.411977 CATCGCTCCTCACCTTCATCT 59.588 52.381 0.00 0.00 0.00 2.90
2442 4787 2.437085 TCGCTCCTCACCTTCATCTA 57.563 50.000 0.00 0.00 0.00 1.98
2443 4788 2.735151 TCGCTCCTCACCTTCATCTAA 58.265 47.619 0.00 0.00 0.00 2.10
2444 4789 3.096852 TCGCTCCTCACCTTCATCTAAA 58.903 45.455 0.00 0.00 0.00 1.85
2445 4790 3.513912 TCGCTCCTCACCTTCATCTAAAA 59.486 43.478 0.00 0.00 0.00 1.52
2446 4791 4.020573 TCGCTCCTCACCTTCATCTAAAAA 60.021 41.667 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.456995 CCTCGTCGCTCCAAGAAGAC 60.457 60.000 0.00 0.00 0.00 3.01
11 12 3.707793 AGAAATCATAACCTCGTCGCTC 58.292 45.455 0.00 0.00 0.00 5.03
17 18 1.787155 CGCCGAGAAATCATAACCTCG 59.213 52.381 0.00 0.00 45.54 4.63
35 36 4.666532 GCCGTCTTGTGTGCACGC 62.667 66.667 23.40 23.40 32.03 5.34
37 38 2.530497 TTCGCCGTCTTGTGTGCAC 61.530 57.895 10.75 10.75 0.00 4.57
52 53 1.223187 ACGCCTAACACCAAAGTTCG 58.777 50.000 0.00 0.00 33.07 3.95
55 56 2.616842 CTGAAACGCCTAACACCAAAGT 59.383 45.455 0.00 0.00 0.00 2.66
67 68 3.428045 CCCTTGAATTGATCTGAAACGCC 60.428 47.826 0.00 0.00 0.00 5.68
68 69 3.191371 ACCCTTGAATTGATCTGAAACGC 59.809 43.478 0.00 0.00 0.00 4.84
69 70 5.048782 TGAACCCTTGAATTGATCTGAAACG 60.049 40.000 0.00 0.00 0.00 3.60
79 80 2.621055 TCACCGTTGAACCCTTGAATTG 59.379 45.455 0.00 0.00 0.00 2.32
95 96 2.544694 CCTAGAGCAGCAATAGTCACCG 60.545 54.545 0.00 0.00 0.00 4.94
104 105 1.375908 CAACGCCCTAGAGCAGCAA 60.376 57.895 0.00 0.00 0.00 3.91
107 108 2.103042 GTGCAACGCCCTAGAGCAG 61.103 63.158 0.00 0.00 35.66 4.24
135 143 2.299582 TGGCCTTGTTGATGACATTTGG 59.700 45.455 3.32 0.00 38.26 3.28
136 144 3.581755 CTGGCCTTGTTGATGACATTTG 58.418 45.455 3.32 0.00 38.26 2.32
137 145 2.564062 CCTGGCCTTGTTGATGACATTT 59.436 45.455 3.32 0.00 38.26 2.32
140 148 0.895100 GCCTGGCCTTGTTGATGACA 60.895 55.000 7.66 0.00 36.19 3.58
155 163 0.762082 TCCTCATAGGAGCTGGCCTG 60.762 60.000 3.32 4.26 40.06 4.85
166 174 1.828832 GTTGTCGTCGCTCCTCATAG 58.171 55.000 0.00 0.00 0.00 2.23
168 176 1.154016 CGTTGTCGTCGCTCCTCAT 60.154 57.895 0.00 0.00 0.00 2.90
179 197 4.117372 GTCGAAGCGCCGTTGTCG 62.117 66.667 2.29 6.23 34.85 4.35
187 205 1.276145 AAAGTGAGTCGTCGAAGCGC 61.276 55.000 0.00 0.00 0.00 5.92
188 206 0.431233 CAAAGTGAGTCGTCGAAGCG 59.569 55.000 0.00 0.00 0.00 4.68
194 212 3.421231 CACTAACGTCAAAGTGAGTCGTC 59.579 47.826 16.51 0.00 44.79 4.20
195 213 3.369385 CACTAACGTCAAAGTGAGTCGT 58.631 45.455 16.51 0.00 44.79 4.34
202 220 3.572584 GATCGACCACTAACGTCAAAGT 58.427 45.455 0.00 0.00 0.00 2.66
205 223 1.135603 CCGATCGACCACTAACGTCAA 60.136 52.381 18.66 0.00 0.00 3.18
213 231 1.183030 TGAACCACCGATCGACCACT 61.183 55.000 18.66 0.00 0.00 4.00
221 239 3.208747 AGAAGTTTGTGAACCACCGAT 57.791 42.857 0.00 0.00 36.39 4.18
287 305 9.784531 ATGAACTCGATGGATTATAAAGTTCAT 57.215 29.630 22.31 22.31 45.01 2.57
305 323 6.631238 TCTTTTCTTTTGCGTAAATGAACTCG 59.369 34.615 21.22 14.35 38.73 4.18
307 325 8.696410 TTTCTTTTCTTTTGCGTAAATGAACT 57.304 26.923 21.22 0.00 38.73 3.01
356 374 5.578776 ACTTTCTTTTCATGGTTTCACGAC 58.421 37.500 0.00 0.00 0.00 4.34
359 377 7.706607 AGCTTTACTTTCTTTTCATGGTTTCAC 59.293 33.333 0.00 0.00 0.00 3.18
407 425 2.094026 CCATGATGACTCGTCAGTTGGA 60.094 50.000 12.85 0.00 43.61 3.53
483 501 5.062308 GTGTCACGCTTAGATTTGTTCTAGG 59.938 44.000 0.00 0.00 38.19 3.02
563 582 4.179298 GAGGATTTGGCTTTTGAGATTGC 58.821 43.478 0.00 0.00 0.00 3.56
608 633 2.612493 CGGATTTGGAGGGTGGGGT 61.612 63.158 0.00 0.00 0.00 4.95
627 652 1.021202 TGAAGTGTTGTGGAAAGCGG 58.979 50.000 0.00 0.00 0.00 5.52
720 745 0.902531 AGAGATTGGTACGTGGTGGG 59.097 55.000 0.00 0.00 0.00 4.61
721 746 2.762535 AAGAGATTGGTACGTGGTGG 57.237 50.000 0.00 0.00 0.00 4.61
722 747 3.364964 GCAAAAGAGATTGGTACGTGGTG 60.365 47.826 0.00 0.00 0.00 4.17
723 748 2.812011 GCAAAAGAGATTGGTACGTGGT 59.188 45.455 0.00 0.00 0.00 4.16
724 749 2.811431 TGCAAAAGAGATTGGTACGTGG 59.189 45.455 0.00 0.00 0.00 4.94
725 750 3.364964 GGTGCAAAAGAGATTGGTACGTG 60.365 47.826 0.00 0.00 0.00 4.49
726 751 2.812011 GGTGCAAAAGAGATTGGTACGT 59.188 45.455 0.00 0.00 0.00 3.57
727 752 2.161609 GGGTGCAAAAGAGATTGGTACG 59.838 50.000 0.00 0.00 0.00 3.67
728 753 2.161609 CGGGTGCAAAAGAGATTGGTAC 59.838 50.000 0.00 0.00 0.00 3.34
729 754 2.039216 TCGGGTGCAAAAGAGATTGGTA 59.961 45.455 0.00 0.00 0.00 3.25
730 755 1.202879 TCGGGTGCAAAAGAGATTGGT 60.203 47.619 0.00 0.00 0.00 3.67
731 756 1.533625 TCGGGTGCAAAAGAGATTGG 58.466 50.000 0.00 0.00 0.00 3.16
732 757 2.293122 TGTTCGGGTGCAAAAGAGATTG 59.707 45.455 0.00 0.00 0.00 2.67
766 1177 1.358877 TTTCTGACGCACCATGATCG 58.641 50.000 0.00 0.00 0.00 3.69
856 1267 4.278669 TGACGGAGCTAATTGGATAGTCTC 59.721 45.833 13.40 2.12 0.00 3.36
860 1271 3.322254 AGGTGACGGAGCTAATTGGATAG 59.678 47.826 0.00 0.00 0.00 2.08
879 1290 5.989777 CGCTTATATACACAGGCTAAAAGGT 59.010 40.000 0.00 0.00 0.00 3.50
919 1330 2.002586 CGGTGTGCAGATAAACCTCAG 58.997 52.381 0.00 0.00 0.00 3.35
981 1392 5.096169 CCCATCGTATTCTAGCGAATAGTG 58.904 45.833 0.00 0.00 41.47 2.74
982 1393 4.158025 CCCCATCGTATTCTAGCGAATAGT 59.842 45.833 0.00 0.00 41.47 2.12
1528 1968 0.669619 CATTCCTGCAGTGCAACACA 59.330 50.000 20.22 3.82 41.43 3.72
1561 2001 2.559668 TGCGCTACTGTACCAAACTACT 59.440 45.455 9.73 0.00 0.00 2.57
1630 2070 3.627395 AGATTACCGAACAATCTGCCA 57.373 42.857 5.62 0.00 40.42 4.92
1640 2080 2.156098 GCCAACCAACAGATTACCGAA 58.844 47.619 0.00 0.00 0.00 4.30
1643 2083 3.649073 GTTTGCCAACCAACAGATTACC 58.351 45.455 0.00 0.00 31.97 2.85
1665 2105 4.156556 TCCATGTTAGACTTCATTGCAAGC 59.843 41.667 4.94 0.00 0.00 4.01
1671 2111 7.824289 TCTCGAAAATCCATGTTAGACTTCATT 59.176 33.333 0.00 0.00 0.00 2.57
1675 2115 7.979444 TTTCTCGAAAATCCATGTTAGACTT 57.021 32.000 0.00 0.00 0.00 3.01
1680 2120 8.289618 CAGAAGTTTTCTCGAAAATCCATGTTA 58.710 33.333 7.95 0.00 41.64 2.41
1682 2122 6.486657 TCAGAAGTTTTCTCGAAAATCCATGT 59.513 34.615 7.95 0.00 41.64 3.21
1683 2123 6.902341 TCAGAAGTTTTCTCGAAAATCCATG 58.098 36.000 7.95 6.22 41.64 3.66
1684 2124 7.609532 AGATCAGAAGTTTTCTCGAAAATCCAT 59.390 33.333 7.95 0.00 41.64 3.41
1686 2126 7.371126 AGATCAGAAGTTTTCTCGAAAATCC 57.629 36.000 7.95 0.00 41.64 3.01
1705 2145 4.202243 TGCCATGACGTGATGAATAGATCA 60.202 41.667 17.08 0.35 43.67 2.92
1706 2146 4.309933 TGCCATGACGTGATGAATAGATC 58.690 43.478 17.08 0.00 0.00 2.75
1719 2159 5.528870 TGTGTTCTATATACTGCCATGACG 58.471 41.667 0.00 0.00 0.00 4.35
1768 2208 9.859427 CAAAACTTTTGCTAAATGATCTATGGA 57.141 29.630 1.30 0.00 0.00 3.41
1769 2209 9.859427 TCAAAACTTTTGCTAAATGATCTATGG 57.141 29.630 9.10 0.00 0.00 2.74
1835 3962 7.879677 TCACGGATCTCTACGGATACTAATTTA 59.120 37.037 0.00 0.00 0.00 1.40
1846 3973 0.029035 CGGTTCACGGATCTCTACGG 59.971 60.000 0.00 0.00 39.42 4.02
1864 3991 7.447374 AACCTAATCATCTGAGATACTCTCG 57.553 40.000 0.00 0.00 46.25 4.04
1881 4008 6.723298 TGATTTCACCACAACAAACCTAAT 57.277 33.333 0.00 0.00 0.00 1.73
1899 4026 5.395214 GGACTTGAACTTTGTGGGTTGATTT 60.395 40.000 0.00 0.00 0.00 2.17
1912 4039 6.176183 CCATTGATGTCTAGGACTTGAACTT 58.824 40.000 0.00 0.00 33.15 2.66
1932 4059 4.806640 AATTCAGGAAAATGCGACCATT 57.193 36.364 0.00 0.00 43.32 3.16
1965 4092 5.544136 TCATTGAACATACACCGTCAATG 57.456 39.130 15.69 15.69 43.11 2.82
1977 4104 6.867662 AGAACGTCTTCTTTCATTGAACAT 57.132 33.333 0.00 0.00 32.29 2.71
1987 4114 5.231568 CGTAGTTGACAAGAACGTCTTCTTT 59.768 40.000 12.05 0.00 43.10 2.52
2026 4153 3.828451 CACATCTTGGGATTGGTGAAGTT 59.172 43.478 0.00 0.00 31.50 2.66
2113 4240 7.709182 GCTCATATATACACACACACTTAACCA 59.291 37.037 0.00 0.00 0.00 3.67
2134 4263 2.674852 CACTACAAACGCAGATGCTCAT 59.325 45.455 2.95 0.00 39.32 2.90
2177 4308 0.466372 TGATCGGCGGTGAGATCTCT 60.466 55.000 22.95 0.19 42.62 3.10
2178 4309 0.600557 ATGATCGGCGGTGAGATCTC 59.399 55.000 16.21 16.21 42.62 2.75
2212 4557 6.292596 GCCATGAACGAGAGATTTATGAACTC 60.293 42.308 0.00 0.00 0.00 3.01
2278 4623 2.301346 GGGTGGCACCTCAATCAATAG 58.699 52.381 33.87 0.00 38.64 1.73
2279 4624 1.408127 CGGGTGGCACCTCAATCAATA 60.408 52.381 33.87 0.00 38.64 1.90
2280 4625 0.680921 CGGGTGGCACCTCAATCAAT 60.681 55.000 33.87 0.00 38.64 2.57
2281 4626 1.303236 CGGGTGGCACCTCAATCAA 60.303 57.895 33.87 0.00 38.64 2.57
2282 4627 2.350895 CGGGTGGCACCTCAATCA 59.649 61.111 33.87 0.00 38.64 2.57
2283 4628 2.438434 CCGGGTGGCACCTCAATC 60.438 66.667 33.87 17.25 38.64 2.67
2284 4629 3.256960 ACCGGGTGGCACCTCAAT 61.257 61.111 33.87 15.86 38.64 2.57
2285 4630 4.263572 CACCGGGTGGCACCTCAA 62.264 66.667 33.87 0.00 38.64 3.02
2296 4641 4.973055 TCAAACGACGCCACCGGG 62.973 66.667 6.32 0.00 39.22 5.73
2297 4642 3.411351 CTCAAACGACGCCACCGG 61.411 66.667 0.00 0.00 39.22 5.28
2298 4643 2.355363 TCTCAAACGACGCCACCG 60.355 61.111 0.00 0.00 41.14 4.94
2299 4644 2.027625 CCTCTCAAACGACGCCACC 61.028 63.158 0.00 0.00 0.00 4.61
2300 4645 0.599204 TTCCTCTCAAACGACGCCAC 60.599 55.000 0.00 0.00 0.00 5.01
2301 4646 0.599204 GTTCCTCTCAAACGACGCCA 60.599 55.000 0.00 0.00 0.00 5.69
2302 4647 0.599204 TGTTCCTCTCAAACGACGCC 60.599 55.000 0.00 0.00 0.00 5.68
2303 4648 1.126846 CATGTTCCTCTCAAACGACGC 59.873 52.381 0.00 0.00 0.00 5.19
2304 4649 1.126846 GCATGTTCCTCTCAAACGACG 59.873 52.381 0.00 0.00 0.00 5.12
2305 4650 1.126846 CGCATGTTCCTCTCAAACGAC 59.873 52.381 0.00 0.00 0.00 4.34
2306 4651 1.428448 CGCATGTTCCTCTCAAACGA 58.572 50.000 0.00 0.00 0.00 3.85
2307 4652 0.179215 GCGCATGTTCCTCTCAAACG 60.179 55.000 0.30 0.00 0.00 3.60
2308 4653 0.179215 CGCGCATGTTCCTCTCAAAC 60.179 55.000 8.75 0.00 0.00 2.93
2309 4654 1.911293 GCGCGCATGTTCCTCTCAAA 61.911 55.000 29.10 0.00 0.00 2.69
2310 4655 2.390599 GCGCGCATGTTCCTCTCAA 61.391 57.895 29.10 0.00 0.00 3.02
2311 4656 2.815211 GCGCGCATGTTCCTCTCA 60.815 61.111 29.10 0.00 0.00 3.27
2312 4657 2.815211 TGCGCGCATGTTCCTCTC 60.815 61.111 33.09 0.00 0.00 3.20
2313 4658 3.121030 GTGCGCGCATGTTCCTCT 61.121 61.111 38.62 0.00 0.00 3.69
2314 4659 4.505217 CGTGCGCGCATGTTCCTC 62.505 66.667 38.29 22.93 0.00 3.71
2319 4664 4.383602 GGAAACGTGCGCGCATGT 62.384 61.111 44.06 44.06 46.85 3.21
2369 4714 9.696917 GAATGTGAGGATTGTTTAGATGTTTTT 57.303 29.630 0.00 0.00 0.00 1.94
2370 4715 8.859090 TGAATGTGAGGATTGTTTAGATGTTTT 58.141 29.630 0.00 0.00 0.00 2.43
2371 4716 8.408043 TGAATGTGAGGATTGTTTAGATGTTT 57.592 30.769 0.00 0.00 0.00 2.83
2372 4717 8.585471 ATGAATGTGAGGATTGTTTAGATGTT 57.415 30.769 0.00 0.00 0.00 2.71
2373 4718 8.051535 AGATGAATGTGAGGATTGTTTAGATGT 58.948 33.333 0.00 0.00 0.00 3.06
2374 4719 8.447924 AGATGAATGTGAGGATTGTTTAGATG 57.552 34.615 0.00 0.00 0.00 2.90
2376 4721 9.958180 TTTAGATGAATGTGAGGATTGTTTAGA 57.042 29.630 0.00 0.00 0.00 2.10
2412 4757 3.694566 GGTGAGGAGCGATGGTAATTTTT 59.305 43.478 0.00 0.00 0.00 1.94
2413 4758 3.054361 AGGTGAGGAGCGATGGTAATTTT 60.054 43.478 0.00 0.00 0.00 1.82
2414 4759 2.505819 AGGTGAGGAGCGATGGTAATTT 59.494 45.455 0.00 0.00 0.00 1.82
2415 4760 2.119495 AGGTGAGGAGCGATGGTAATT 58.881 47.619 0.00 0.00 0.00 1.40
2416 4761 1.794714 AGGTGAGGAGCGATGGTAAT 58.205 50.000 0.00 0.00 0.00 1.89
2417 4762 1.480954 GAAGGTGAGGAGCGATGGTAA 59.519 52.381 0.00 0.00 0.00 2.85
2418 4763 1.112113 GAAGGTGAGGAGCGATGGTA 58.888 55.000 0.00 0.00 0.00 3.25
2419 4764 0.904865 TGAAGGTGAGGAGCGATGGT 60.905 55.000 0.00 0.00 0.00 3.55
2420 4765 0.467384 ATGAAGGTGAGGAGCGATGG 59.533 55.000 0.00 0.00 0.00 3.51
2421 4766 1.411977 AGATGAAGGTGAGGAGCGATG 59.588 52.381 0.00 0.00 0.00 3.84
2422 4767 1.786937 AGATGAAGGTGAGGAGCGAT 58.213 50.000 0.00 0.00 0.00 4.58
2423 4768 2.437085 TAGATGAAGGTGAGGAGCGA 57.563 50.000 0.00 0.00 0.00 4.93
2424 4769 3.526931 TTTAGATGAAGGTGAGGAGCG 57.473 47.619 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.