Multiple sequence alignment - TraesCS1D01G303100

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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 TraesCS1D01G303100 chr1D 100.000 2630 0 0 1 2630 400957531 400954902 0.000000e+00 4857.0
1 TraesCS1D01G303100 chr1B 92.780 1759 64 30 558 2306 538165749 538164044 0.000000e+00 2486.0
2 TraesCS1D01G303100 chr1B 90.351 228 17 5 2407 2630 538164005 538163779 7.120000e-76 294.0
3 TraesCS1D01G303100 chr1B 79.027 329 30 19 218 543 538166026 538165734 3.460000e-44 189.0
4 TraesCS1D01G303100 chr1A 90.228 1883 75 39 568 2441 497193169 497191387 0.000000e+00 2357.0
5 TraesCS1D01G303100 chr1A 86.127 519 47 17 24 530 497193681 497193176 1.070000e-148 536.0
6 TraesCS1D01G303100 chr1A 90.816 196 13 5 2435 2626 497191261 497191067 9.340000e-65 257.0
7 TraesCS1D01G303100 chr4D 76.410 195 26 13 1085 1263 102534312 102534122 1.300000e-13 87.9
8 TraesCS1D01G303100 chr4D 94.595 37 1 1 2276 2312 370688394 370688429 3.660000e-04 56.5
9 TraesCS1D01G303100 chr4B 82.759 87 15 0 1085 1171 147066773 147066687 7.800000e-11 78.7
10 TraesCS1D01G303100 chr2B 94.737 38 2 0 2273 2310 549502467 549502504 2.830000e-05 60.2
11 TraesCS1D01G303100 chr2D 97.143 35 0 1 2273 2307 470439049 470439082 1.020000e-04 58.4
12 TraesCS1D01G303100 chr5B 94.595 37 0 2 2274 2310 698011521 698011555 3.660000e-04 56.5
13 TraesCS1D01G303100 chr7A 100.000 28 0 0 2459 2486 410601806 410601833 5.000000e-03 52.8
14 TraesCS1D01G303100 chr6B 100.000 28 0 0 2459 2486 546528507 546528480 5.000000e-03 52.8


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 TraesCS1D01G303100 chr1D 400954902 400957531 2629 True 4857.000000 4857 100.000 1 2630 1 chr1D.!!$R1 2629
1 TraesCS1D01G303100 chr1B 538163779 538166026 2247 True 989.666667 2486 87.386 218 2630 3 chr1B.!!$R1 2412
2 TraesCS1D01G303100 chr1A 497191067 497193681 2614 True 1050.000000 2357 89.057 24 2626 3 chr1A.!!$R1 2602

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
159 163 0.032952 GCGTGACCATTCGCCCTATA 59.967 55.0 0.0 0.0 45.54 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2192 0.890996 GATCATTGGCCGGCCCTTAG 60.891 60.0 41.75 27.54 34.56 2.18 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
59 63 6.128363 CCGAAAAGAGGGTTGAAACATAGTAC 60.128 42.308 0.00 0.00 0.00 2.73
71 75 9.730420 GTTGAAACATAGTACAAGATTTGTTGT 57.270 29.630 0.00 0.00 42.22 3.32
87 91 8.084073 AGATTTGTTGTTGTTCTATTCACATGG 58.916 33.333 0.00 0.00 0.00 3.66
116 120 2.803386 TCGTTTTCTCGCAAACATGCTA 59.197 40.909 0.00 0.00 36.58 3.49
117 121 3.248841 TCGTTTTCTCGCAAACATGCTAA 59.751 39.130 0.00 0.00 36.58 3.09
142 146 0.174845 TGTTAGGTGGATCGAAGGCG 59.825 55.000 0.00 0.00 39.35 5.52
143 147 0.175073 GTTAGGTGGATCGAAGGCGT 59.825 55.000 0.00 0.00 38.98 5.68
144 148 0.174845 TTAGGTGGATCGAAGGCGTG 59.825 55.000 0.00 0.00 38.98 5.34
145 149 0.681887 TAGGTGGATCGAAGGCGTGA 60.682 55.000 0.00 0.00 38.98 4.35
146 150 1.810030 GGTGGATCGAAGGCGTGAC 60.810 63.158 0.00 0.00 38.98 3.67
147 151 1.810030 GTGGATCGAAGGCGTGACC 60.810 63.158 0.00 0.00 38.98 4.02
148 152 2.279810 TGGATCGAAGGCGTGACCA 61.280 57.895 0.00 0.00 43.14 4.02
149 153 1.144057 GGATCGAAGGCGTGACCAT 59.856 57.895 0.00 0.00 43.14 3.55
150 154 0.462047 GGATCGAAGGCGTGACCATT 60.462 55.000 0.00 0.00 43.14 3.16
151 155 0.931005 GATCGAAGGCGTGACCATTC 59.069 55.000 0.00 0.00 43.14 2.67
152 156 0.806102 ATCGAAGGCGTGACCATTCG 60.806 55.000 12.31 12.31 44.03 3.34
157 161 2.185867 GCGTGACCATTCGCCCTA 59.814 61.111 0.00 0.00 45.54 3.53
158 162 1.227556 GCGTGACCATTCGCCCTAT 60.228 57.895 0.00 0.00 45.54 2.57
159 163 0.032952 GCGTGACCATTCGCCCTATA 59.967 55.000 0.00 0.00 45.54 1.31
160 164 1.935300 GCGTGACCATTCGCCCTATAG 60.935 57.143 0.00 0.00 45.54 1.31
161 165 1.797025 GTGACCATTCGCCCTATAGC 58.203 55.000 0.00 0.00 0.00 2.97
168 172 1.568504 TTCGCCCTATAGCCCTATGG 58.431 55.000 0.00 0.00 0.00 2.74
171 175 1.657804 GCCCTATAGCCCTATGGTGT 58.342 55.000 0.00 0.00 0.00 4.16
203 216 2.887783 TGGTCGCATCTCTATCTTCTCC 59.112 50.000 0.00 0.00 0.00 3.71
207 220 3.500299 TCGCATCTCTATCTTCTCCTTCG 59.500 47.826 0.00 0.00 0.00 3.79
212 225 6.150307 GCATCTCTATCTTCTCCTTCGTCATA 59.850 42.308 0.00 0.00 0.00 2.15
251 265 3.322466 CCGGCACCACTCCTCCTT 61.322 66.667 0.00 0.00 0.00 3.36
256 270 0.398318 GCACCACTCCTCCTTTGTCT 59.602 55.000 0.00 0.00 0.00 3.41
376 390 8.603181 ACACAAGAAAACAAACATAATTTCAGC 58.397 29.630 0.00 0.00 34.91 4.26
390 404 2.736144 TTCAGCACCACTTACCTACG 57.264 50.000 0.00 0.00 0.00 3.51
409 423 2.818274 GTCCGGTGCGACCATTCC 60.818 66.667 0.00 0.00 38.47 3.01
412 426 1.969064 CCGGTGCGACCATTCCAAA 60.969 57.895 0.00 0.00 38.47 3.28
421 436 2.031683 CGACCATTCCAAATCTAACCGC 59.968 50.000 0.00 0.00 0.00 5.68
543 565 6.875195 CACATTAATTTGGGTCTGCAGAAAAT 59.125 34.615 20.19 17.54 0.00 1.82
545 567 7.388500 ACATTAATTTGGGTCTGCAGAAAATTG 59.612 33.333 30.40 22.74 33.67 2.32
546 568 4.961438 ATTTGGGTCTGCAGAAAATTGT 57.039 36.364 20.19 0.73 0.00 2.71
550 572 3.703556 TGGGTCTGCAGAAAATTGTCAAA 59.296 39.130 20.19 0.00 0.00 2.69
551 573 4.161189 TGGGTCTGCAGAAAATTGTCAAAA 59.839 37.500 20.19 0.00 0.00 2.44
552 574 5.115480 GGGTCTGCAGAAAATTGTCAAAAA 58.885 37.500 20.19 0.00 0.00 1.94
574 596 4.590850 AAAATTGGGTCTGCAGAAAGTC 57.409 40.909 20.19 5.66 0.00 3.01
575 597 2.957402 ATTGGGTCTGCAGAAAGTCA 57.043 45.000 20.19 11.36 0.00 3.41
576 598 2.957402 TTGGGTCTGCAGAAAGTCAT 57.043 45.000 20.19 0.00 0.00 3.06
577 599 4.574674 ATTGGGTCTGCAGAAAGTCATA 57.425 40.909 20.19 0.72 0.00 2.15
578 600 4.574674 TTGGGTCTGCAGAAAGTCATAT 57.425 40.909 20.19 0.00 0.00 1.78
579 601 3.877559 TGGGTCTGCAGAAAGTCATATG 58.122 45.455 20.19 0.00 0.00 1.78
580 602 3.264193 TGGGTCTGCAGAAAGTCATATGT 59.736 43.478 20.19 0.00 0.00 2.29
607 629 5.083821 ACCCACCAATTAAGTGTTGCTTAT 58.916 37.500 1.80 0.00 39.23 1.73
787 809 2.858745 CCCACCCAACCTAATTATCCG 58.141 52.381 0.00 0.00 0.00 4.18
890 912 0.256752 TCGTCTCCACCGATCCCTTA 59.743 55.000 0.00 0.00 0.00 2.69
921 944 2.331132 GCAGCAGCTCTTGGGTCAC 61.331 63.158 0.00 0.00 37.91 3.67
922 945 1.673665 CAGCAGCTCTTGGGTCACC 60.674 63.158 0.00 0.00 37.24 4.02
923 946 1.845205 AGCAGCTCTTGGGTCACCT 60.845 57.895 0.00 0.00 37.76 4.00
924 947 1.376553 GCAGCTCTTGGGTCACCTC 60.377 63.158 0.00 0.00 37.76 3.85
925 948 1.835927 GCAGCTCTTGGGTCACCTCT 61.836 60.000 0.00 0.00 37.76 3.69
975 998 2.500098 TCTAGGTTTCTTGATCCACCGG 59.500 50.000 0.00 0.00 34.19 5.28
976 999 1.064825 AGGTTTCTTGATCCACCGGT 58.935 50.000 0.00 0.00 34.19 5.28
977 1000 1.003233 AGGTTTCTTGATCCACCGGTC 59.997 52.381 2.59 0.00 34.19 4.79
978 1001 1.003233 GGTTTCTTGATCCACCGGTCT 59.997 52.381 2.59 0.00 0.00 3.85
979 1002 2.235402 GGTTTCTTGATCCACCGGTCTA 59.765 50.000 2.59 0.00 0.00 2.59
990 1013 3.009916 TCCACCGGTCTAGTCTAGTCTTT 59.990 47.826 2.59 0.00 0.00 2.52
1650 1673 1.391157 GCCACTGAAACTGGGTTGCA 61.391 55.000 0.00 0.00 29.55 4.08
1657 1680 2.238521 GAAACTGGGTTGCATCCTTCA 58.761 47.619 13.47 3.49 0.00 3.02
1664 1687 1.994779 GGTTGCATCCTTCAATTTGCG 59.005 47.619 6.56 0.00 37.92 4.85
1665 1688 1.391144 GTTGCATCCTTCAATTTGCGC 59.609 47.619 0.00 0.00 37.92 6.09
1666 1689 0.889994 TGCATCCTTCAATTTGCGCT 59.110 45.000 9.73 0.00 37.92 5.92
1668 1691 1.800286 GCATCCTTCAATTTGCGCTCC 60.800 52.381 9.73 0.00 0.00 4.70
1669 1692 1.106285 ATCCTTCAATTTGCGCTCCC 58.894 50.000 9.73 0.00 0.00 4.30
1670 1693 0.038166 TCCTTCAATTTGCGCTCCCT 59.962 50.000 9.73 0.00 0.00 4.20
1671 1694 0.890683 CCTTCAATTTGCGCTCCCTT 59.109 50.000 9.73 0.00 0.00 3.95
1672 1695 1.273327 CCTTCAATTTGCGCTCCCTTT 59.727 47.619 9.73 0.00 0.00 3.11
1673 1696 2.289010 CCTTCAATTTGCGCTCCCTTTT 60.289 45.455 9.73 0.00 0.00 2.27
1674 1697 2.723124 TCAATTTGCGCTCCCTTTTC 57.277 45.000 9.73 0.00 0.00 2.29
1675 1698 2.238521 TCAATTTGCGCTCCCTTTTCT 58.761 42.857 9.73 0.00 0.00 2.52
1676 1699 2.627699 TCAATTTGCGCTCCCTTTTCTT 59.372 40.909 9.73 0.00 0.00 2.52
1677 1700 2.989166 CAATTTGCGCTCCCTTTTCTTC 59.011 45.455 9.73 0.00 0.00 2.87
1678 1701 0.958822 TTTGCGCTCCCTTTTCTTCC 59.041 50.000 9.73 0.00 0.00 3.46
1679 1702 0.179004 TTGCGCTCCCTTTTCTTCCA 60.179 50.000 9.73 0.00 0.00 3.53
1680 1703 0.606401 TGCGCTCCCTTTTCTTCCAG 60.606 55.000 9.73 0.00 0.00 3.86
1723 1746 1.302351 AGCAGAACAGCTCCTGTGC 60.302 57.895 5.73 5.73 44.62 4.57
1739 1763 3.855853 GCGCCCCCTTCTCTCTCC 61.856 72.222 0.00 0.00 0.00 3.71
1971 1997 2.074576 TCACTGTCTACGTTCTCTCCG 58.925 52.381 0.00 0.00 0.00 4.63
1976 2002 3.930336 TGTCTACGTTCTCTCCGACTTA 58.070 45.455 0.00 0.00 0.00 2.24
2020 2050 5.305585 TCAAAGTTAGCTGAAATTCTCCGT 58.694 37.500 0.00 0.00 0.00 4.69
2045 2076 7.672983 TGTAGAATCTGAAATCTGAACCAAC 57.327 36.000 0.00 0.00 0.00 3.77
2104 2140 3.736433 CGTAGCAAGCAGTCTAGCAGAAT 60.736 47.826 0.00 0.00 36.85 2.40
2135 2171 3.877357 TCGACCAGCTAGCGCTCG 61.877 66.667 16.34 19.59 45.15 5.03
2148 2184 2.105930 GCTCGCTCCAGCCAGTAG 59.894 66.667 0.00 0.00 37.91 2.57
2149 2185 2.716017 GCTCGCTCCAGCCAGTAGT 61.716 63.158 0.00 0.00 37.91 2.73
2150 2186 1.384989 GCTCGCTCCAGCCAGTAGTA 61.385 60.000 0.00 0.00 37.91 1.82
2151 2187 0.665835 CTCGCTCCAGCCAGTAGTAG 59.334 60.000 0.00 0.00 37.91 2.57
2152 2188 1.066587 CGCTCCAGCCAGTAGTAGC 59.933 63.158 0.00 0.00 37.91 3.58
2153 2189 1.388065 CGCTCCAGCCAGTAGTAGCT 61.388 60.000 0.00 0.00 40.89 3.32
2154 2190 1.693627 GCTCCAGCCAGTAGTAGCTA 58.306 55.000 0.00 0.00 37.18 3.32
2155 2191 1.611491 GCTCCAGCCAGTAGTAGCTAG 59.389 57.143 0.00 0.00 37.18 3.42
2156 2192 1.611491 CTCCAGCCAGTAGTAGCTAGC 59.389 57.143 6.62 6.62 37.18 3.42
2157 2193 1.215673 TCCAGCCAGTAGTAGCTAGCT 59.784 52.381 23.12 23.12 37.18 3.32
2158 2194 2.442126 TCCAGCCAGTAGTAGCTAGCTA 59.558 50.000 20.67 20.67 37.18 3.32
2161 2197 3.254657 CAGCCAGTAGTAGCTAGCTAAGG 59.745 52.174 25.74 20.63 37.18 2.69
2189 2225 2.036958 ATGATCCGCGTTGAATTCCA 57.963 45.000 4.92 0.00 0.00 3.53
2252 2288 1.425066 CTGGTGTATGTGGGCCCATAT 59.575 52.381 33.59 33.59 30.47 1.78
2267 2303 3.807209 GCCCATATGCCAGTAAGAACGAT 60.807 47.826 0.00 0.00 0.00 3.73
2279 2315 7.925993 CCAGTAAGAACGATTGGCATTATTTA 58.074 34.615 0.00 0.00 0.00 1.40
2335 2371 5.826737 CAGCAATGGAGAATATTTCCTGTCT 59.173 40.000 14.07 0.00 35.67 3.41
2377 2413 0.321021 GCCATGGCCACAAAATGACA 59.679 50.000 27.24 0.00 34.56 3.58
2379 2415 1.894466 CCATGGCCACAAAATGACAGA 59.106 47.619 8.16 0.00 0.00 3.41
2398 2434 6.939730 TGACAGATTGGTCAAGCAAACTTATA 59.060 34.615 2.44 0.00 44.34 0.98
2487 2654 4.141287 ACTGTATACTGCAAGGCAACAAA 58.859 39.130 9.48 0.00 38.41 2.83
2489 2656 3.254657 TGTATACTGCAAGGCAACAAACC 59.745 43.478 4.17 0.00 38.41 3.27
2502 2669 4.048504 GCAACAAACCCACAATCAAGTAC 58.951 43.478 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.739498 TGTACTATGTTTCAACCCTCTTTTC 57.261 36.000 0.00 0.00 0.00 2.29
41 42 7.923414 AATCTTGTACTATGTTTCAACCCTC 57.077 36.000 0.00 0.00 0.00 4.30
42 43 7.724061 ACAAATCTTGTACTATGTTTCAACCCT 59.276 33.333 0.00 0.00 43.27 4.34
43 44 7.882179 ACAAATCTTGTACTATGTTTCAACCC 58.118 34.615 0.00 0.00 43.27 4.11
59 63 8.854979 TGTGAATAGAACAACAACAAATCTTG 57.145 30.769 0.00 0.00 0.00 3.02
68 72 5.781210 TTGCCATGTGAATAGAACAACAA 57.219 34.783 0.00 0.00 0.00 2.83
71 75 7.116090 CGAAAATTTGCCATGTGAATAGAACAA 59.884 33.333 0.00 0.00 0.00 2.83
79 83 5.814705 AGAAAACGAAAATTTGCCATGTGAA 59.185 32.000 0.00 0.00 0.00 3.18
87 91 4.430407 TTGCGAGAAAACGAAAATTTGC 57.570 36.364 0.00 0.00 35.09 3.68
117 121 4.760204 CCTTCGATCCACCTAACAGTTTTT 59.240 41.667 0.00 0.00 0.00 1.94
127 131 1.982395 TCACGCCTTCGATCCACCT 60.982 57.895 0.00 0.00 39.41 4.00
142 146 1.608283 GGCTATAGGGCGAATGGTCAC 60.608 57.143 1.04 0.00 0.00 3.67
143 147 0.685097 GGCTATAGGGCGAATGGTCA 59.315 55.000 1.04 0.00 0.00 4.02
144 148 0.036294 GGGCTATAGGGCGAATGGTC 60.036 60.000 1.04 0.00 41.87 4.02
145 149 0.473886 AGGGCTATAGGGCGAATGGT 60.474 55.000 1.04 0.00 41.87 3.55
146 150 1.568504 TAGGGCTATAGGGCGAATGG 58.431 55.000 1.04 0.00 41.87 3.16
147 151 2.158900 CCATAGGGCTATAGGGCGAATG 60.159 54.545 1.04 2.99 41.87 2.67
148 152 2.119495 CCATAGGGCTATAGGGCGAAT 58.881 52.381 1.04 0.00 41.87 3.34
149 153 1.203262 ACCATAGGGCTATAGGGCGAA 60.203 52.381 1.04 0.00 41.87 4.70
150 154 0.412244 ACCATAGGGCTATAGGGCGA 59.588 55.000 1.04 0.00 41.87 5.54
151 155 0.537188 CACCATAGGGCTATAGGGCG 59.463 60.000 1.04 0.00 41.87 6.13
152 156 1.279271 CACACCATAGGGCTATAGGGC 59.721 57.143 1.04 0.00 37.90 5.19
153 157 2.567615 GTCACACCATAGGGCTATAGGG 59.432 54.545 1.04 0.00 37.90 3.53
154 158 3.006967 GTGTCACACCATAGGGCTATAGG 59.993 52.174 0.00 0.00 37.90 2.57
155 159 4.258702 GTGTCACACCATAGGGCTATAG 57.741 50.000 0.00 0.00 37.90 1.31
183 196 3.153919 AGGAGAAGATAGAGATGCGACC 58.846 50.000 0.00 0.00 0.00 4.79
203 216 3.553511 GTGGAGATTGTGCTATGACGAAG 59.446 47.826 0.00 0.00 0.00 3.79
207 220 2.565841 GGGTGGAGATTGTGCTATGAC 58.434 52.381 0.00 0.00 0.00 3.06
212 225 3.090765 GGGGGTGGAGATTGTGCT 58.909 61.111 0.00 0.00 0.00 4.40
251 265 0.888619 AGAAGCGATGACGGAGACAA 59.111 50.000 0.00 0.00 40.15 3.18
256 270 1.139734 GCAGAGAAGCGATGACGGA 59.860 57.895 0.00 0.00 40.15 4.69
320 334 5.277857 AGTCATTATAGGTAGTGTGTGCC 57.722 43.478 0.00 0.00 0.00 5.01
350 364 8.603181 GCTGAAATTATGTTTGTTTTCTTGTGT 58.397 29.630 0.00 0.00 0.00 3.72
352 366 8.603181 GTGCTGAAATTATGTTTGTTTTCTTGT 58.397 29.630 0.00 0.00 0.00 3.16
376 390 1.131883 CGGACTCGTAGGTAAGTGGTG 59.868 57.143 0.00 0.00 0.00 4.17
390 404 1.810030 GAATGGTCGCACCGGACTC 60.810 63.158 9.46 0.00 42.58 3.36
409 423 1.664151 GACCTTCCGCGGTTAGATTTG 59.336 52.381 27.15 12.64 37.42 2.32
412 426 1.436336 CGACCTTCCGCGGTTAGAT 59.564 57.895 27.15 11.17 37.42 1.98
464 482 0.026027 GTCTCGAGTGCGGTAGTACG 59.974 60.000 13.13 0.00 38.06 3.67
470 488 1.452953 TTCACAGTCTCGAGTGCGGT 61.453 55.000 13.13 10.55 38.28 5.68
478 496 4.149571 CACTCATGACTTTTCACAGTCTCG 59.850 45.833 0.00 0.00 43.32 4.04
552 574 4.405358 TGACTTTCTGCAGACCCAATTTTT 59.595 37.500 18.03 0.00 0.00 1.94
553 575 3.960102 TGACTTTCTGCAGACCCAATTTT 59.040 39.130 18.03 0.00 0.00 1.82
554 576 3.565307 TGACTTTCTGCAGACCCAATTT 58.435 40.909 18.03 0.00 0.00 1.82
555 577 3.228188 TGACTTTCTGCAGACCCAATT 57.772 42.857 18.03 2.23 0.00 2.32
556 578 2.957402 TGACTTTCTGCAGACCCAAT 57.043 45.000 18.03 0.00 0.00 3.16
557 579 2.957402 ATGACTTTCTGCAGACCCAA 57.043 45.000 18.03 7.58 0.00 4.12
558 580 3.264193 ACATATGACTTTCTGCAGACCCA 59.736 43.478 18.03 12.04 0.00 4.51
559 581 3.624861 CACATATGACTTTCTGCAGACCC 59.375 47.826 18.03 6.40 0.00 4.46
560 582 4.256920 ACACATATGACTTTCTGCAGACC 58.743 43.478 18.03 6.78 0.00 3.85
561 583 6.183360 GGTTACACATATGACTTTCTGCAGAC 60.183 42.308 18.03 5.40 0.00 3.51
562 584 5.874810 GGTTACACATATGACTTTCTGCAGA 59.125 40.000 13.74 13.74 0.00 4.26
563 585 5.065218 GGGTTACACATATGACTTTCTGCAG 59.935 44.000 10.38 7.63 0.00 4.41
564 586 4.941263 GGGTTACACATATGACTTTCTGCA 59.059 41.667 10.38 0.00 0.00 4.41
565 587 4.941263 TGGGTTACACATATGACTTTCTGC 59.059 41.667 10.38 0.00 0.00 4.26
579 601 9.504793 AAGCAACACTTAATTGGTGGGTTACAC 62.505 40.741 12.26 0.00 42.62 2.90
580 602 4.038162 GCAACACTTAATTGGTGGGTTACA 59.962 41.667 12.26 0.00 38.83 2.41
787 809 1.077429 GTGGACAGGAATGCCCCTC 60.077 63.158 0.00 0.00 33.38 4.30
890 912 1.609208 CTGCTGCTGGTTGGTTTACT 58.391 50.000 0.00 0.00 0.00 2.24
917 940 1.326951 GCAGGGAGAGGAGAGGTGAC 61.327 65.000 0.00 0.00 0.00 3.67
921 944 1.457455 GGAGCAGGGAGAGGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
922 945 0.468029 GAGGAGCAGGGAGAGGAGAG 60.468 65.000 0.00 0.00 0.00 3.20
923 946 1.618030 GAGGAGCAGGGAGAGGAGA 59.382 63.158 0.00 0.00 0.00 3.71
924 947 1.827789 CGAGGAGCAGGGAGAGGAG 60.828 68.421 0.00 0.00 0.00 3.69
925 948 1.650242 ATCGAGGAGCAGGGAGAGGA 61.650 60.000 0.00 0.00 0.00 3.71
975 998 5.163632 GGCCACACTAAAGACTAGACTAGAC 60.164 48.000 16.55 10.06 0.00 2.59
976 999 4.948621 GGCCACACTAAAGACTAGACTAGA 59.051 45.833 16.55 0.00 0.00 2.43
977 1000 4.705507 TGGCCACACTAAAGACTAGACTAG 59.294 45.833 0.00 8.00 0.00 2.57
978 1001 4.669700 TGGCCACACTAAAGACTAGACTA 58.330 43.478 0.00 0.00 0.00 2.59
979 1002 3.507411 TGGCCACACTAAAGACTAGACT 58.493 45.455 0.00 0.00 0.00 3.24
990 1013 1.078497 CTTCGCCATGGCCACACTA 60.078 57.895 30.79 8.80 37.98 2.74
1612 1635 3.111939 CTACGAGGACCAGCTCCG 58.888 66.667 0.00 0.00 45.10 4.63
1650 1673 1.106285 GGGAGCGCAAATTGAAGGAT 58.894 50.000 11.47 0.00 0.00 3.24
1657 1680 2.029020 GGAAGAAAAGGGAGCGCAAATT 60.029 45.455 11.47 0.00 0.00 1.82
1664 1687 2.558795 GGAAACTGGAAGAAAAGGGAGC 59.441 50.000 0.00 0.00 37.43 4.70
1665 1688 2.814336 CGGAAACTGGAAGAAAAGGGAG 59.186 50.000 0.00 0.00 37.43 4.30
1666 1689 2.440253 TCGGAAACTGGAAGAAAAGGGA 59.560 45.455 0.00 0.00 37.43 4.20
1668 1691 3.211045 TGTCGGAAACTGGAAGAAAAGG 58.789 45.455 0.00 0.00 37.43 3.11
1669 1692 5.215160 CAATGTCGGAAACTGGAAGAAAAG 58.785 41.667 0.00 0.00 37.43 2.27
1670 1693 4.642885 ACAATGTCGGAAACTGGAAGAAAA 59.357 37.500 0.00 0.00 37.43 2.29
1671 1694 4.204012 ACAATGTCGGAAACTGGAAGAAA 58.796 39.130 0.00 0.00 37.43 2.52
1672 1695 3.815809 ACAATGTCGGAAACTGGAAGAA 58.184 40.909 0.00 0.00 37.43 2.52
1673 1696 3.485463 ACAATGTCGGAAACTGGAAGA 57.515 42.857 0.00 0.00 37.43 2.87
1674 1697 4.290155 CAAACAATGTCGGAAACTGGAAG 58.710 43.478 0.00 0.00 42.29 3.46
1675 1698 3.067461 CCAAACAATGTCGGAAACTGGAA 59.933 43.478 0.00 0.00 0.00 3.53
1676 1699 2.621055 CCAAACAATGTCGGAAACTGGA 59.379 45.455 0.00 0.00 0.00 3.86
1677 1700 2.288152 CCCAAACAATGTCGGAAACTGG 60.288 50.000 3.62 0.00 0.00 4.00
1678 1701 2.862140 GCCCAAACAATGTCGGAAACTG 60.862 50.000 3.62 0.00 0.00 3.16
1679 1702 1.339929 GCCCAAACAATGTCGGAAACT 59.660 47.619 3.62 0.00 0.00 2.66
1680 1703 1.604438 GGCCCAAACAATGTCGGAAAC 60.604 52.381 3.62 0.00 0.00 2.78
1723 1746 1.268283 AAAGGAGAGAGAAGGGGGCG 61.268 60.000 0.00 0.00 0.00 6.13
1895 1919 9.841295 AGTAGGAGTAATACACAACTTCAAAAA 57.159 29.630 0.00 0.00 0.00 1.94
1896 1920 9.841295 AAGTAGGAGTAATACACAACTTCAAAA 57.159 29.630 0.00 0.00 0.00 2.44
1897 1921 9.485206 GAAGTAGGAGTAATACACAACTTCAAA 57.515 33.333 19.75 0.00 40.64 2.69
1898 1922 8.867097 AGAAGTAGGAGTAATACACAACTTCAA 58.133 33.333 23.19 0.00 42.42 2.69
1899 1923 8.418597 AGAAGTAGGAGTAATACACAACTTCA 57.581 34.615 23.19 0.00 42.42 3.02
1928 1954 3.402628 TTGGCCTACTGTGACTTCTTC 57.597 47.619 3.32 0.00 0.00 2.87
1940 1966 3.617263 CGTAGACAGTGAAATTGGCCTAC 59.383 47.826 3.32 0.00 27.27 3.18
1971 1997 1.135286 GCCTTTGGTGCTGCATAAGTC 60.135 52.381 5.27 0.00 0.00 3.01
1976 2002 1.123246 AAAGGCCTTTGGTGCTGCAT 61.123 50.000 29.91 0.94 0.00 3.96
2020 2050 7.939039 AGTTGGTTCAGATTTCAGATTCTACAA 59.061 33.333 0.00 0.00 0.00 2.41
2045 2076 2.671177 CGGCCTCTTTGACACGCAG 61.671 63.158 0.00 0.00 0.00 5.18
2104 2140 2.037136 GTCGACCGAGGAAGTCCGA 61.037 63.158 3.51 0.00 42.08 4.55
2135 2171 1.611491 CTAGCTACTACTGGCTGGAGC 59.389 57.143 3.14 3.05 38.96 4.70
2143 2179 2.559231 GGCCCTTAGCTAGCTACTACTG 59.441 54.545 24.09 11.78 43.05 2.74
2148 2184 1.666580 CCGGCCCTTAGCTAGCTAC 59.333 63.158 24.09 12.31 43.05 3.58
2149 2185 2.207924 GCCGGCCCTTAGCTAGCTA 61.208 63.158 20.67 20.67 43.05 3.32
2150 2186 3.551407 GCCGGCCCTTAGCTAGCT 61.551 66.667 23.12 23.12 43.05 3.32
2151 2187 4.627801 GGCCGGCCCTTAGCTAGC 62.628 72.222 36.64 6.62 43.05 3.42
2152 2188 2.056906 ATTGGCCGGCCCTTAGCTAG 62.057 60.000 41.75 0.00 43.05 3.42
2153 2189 2.076184 ATTGGCCGGCCCTTAGCTA 61.076 57.895 41.75 19.95 43.05 3.32
2154 2190 3.420482 ATTGGCCGGCCCTTAGCT 61.420 61.111 41.75 17.21 43.05 3.32
2155 2191 2.983725 ATCATTGGCCGGCCCTTAGC 62.984 60.000 41.75 17.44 42.60 3.09
2156 2192 0.890996 GATCATTGGCCGGCCCTTAG 60.891 60.000 41.75 27.54 34.56 2.18
2157 2193 1.150536 GATCATTGGCCGGCCCTTA 59.849 57.895 41.75 27.10 34.56 2.69
2158 2194 2.123726 GATCATTGGCCGGCCCTT 60.124 61.111 41.75 26.62 34.56 3.95
2283 2319 6.497437 GCAAATCTTTTGCCTTGTTTCAAAT 58.503 32.000 12.74 0.00 39.38 2.32
2335 2371 7.504238 TGGCTGGTTTCAAATAAGTTTTCTCTA 59.496 33.333 0.00 0.00 0.00 2.43
2379 2415 9.030452 TGGTAAATATAAGTTTGCTTGACCAAT 57.970 29.630 0.00 0.00 36.22 3.16
2487 2654 8.472007 TTGATTTTTAGTACTTGATTGTGGGT 57.528 30.769 0.00 0.00 0.00 4.51
2489 2656 8.901748 CGTTTGATTTTTAGTACTTGATTGTGG 58.098 33.333 0.00 0.00 0.00 4.17
2502 2669 8.557029 ACTTCTTGTACTCCGTTTGATTTTTAG 58.443 33.333 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.