Multiple sequence alignment - TraesCS3B01G317500

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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 TraesCS3B01G317500 chr3B 100.000 2671 0 0 1 2671 511070108 511072778 0.000000e+00 4933.0
1 TraesCS3B01G317500 chr3D 89.150 1106 58 29 859 1942 392054218 392055283 0.000000e+00 1321.0
2 TraesCS3B01G317500 chr3D 92.247 632 36 9 2039 2665 392055554 392056177 0.000000e+00 883.0
3 TraesCS3B01G317500 chr3D 90.476 483 24 7 184 661 392053303 392053768 3.780000e-173 617.0
4 TraesCS3B01G317500 chr3D 89.888 178 9 7 654 828 392054049 392054220 1.240000e-53 220.0
5 TraesCS3B01G317500 chr3D 96.190 105 2 2 1 105 392053194 392053296 1.270000e-38 171.0
6 TraesCS3B01G317500 chr3D 82.609 115 1 3 1948 2043 392055415 392055529 1.700000e-12 84.2
7 TraesCS3B01G317500 chr3A 93.222 841 38 9 814 1638 512307771 512308608 0.000000e+00 1219.0
8 TraesCS3B01G317500 chr3A 85.110 544 40 20 1 532 512306760 512307274 3.940000e-143 518.0
9 TraesCS3B01G317500 chr3A 88.337 403 33 8 2074 2472 512309182 512309574 3.110000e-129 472.0
10 TraesCS3B01G317500 chr3A 89.899 198 12 4 2471 2668 512309733 512309922 5.710000e-62 248.0
11 TraesCS3B01G317500 chr3A 83.505 194 10 7 1673 1866 512308778 512308949 7.650000e-36 161.0
12 TraesCS3B01G317500 chr3A 81.757 148 10 5 656 801 512307655 512307787 1.010000e-19 108.0
13 TraesCS3B01G317500 chr3A 95.833 48 1 1 1997 2043 512309082 512309129 2.850000e-10 76.8
14 TraesCS3B01G317500 chr1D 77.647 170 23 10 1299 1453 439305814 439305983 3.660000e-14 89.8
15 TraesCS3B01G317500 chr1B 77.647 170 23 9 1299 1453 596038897 596039066 3.660000e-14 89.8
16 TraesCS3B01G317500 chr1A 77.108 166 23 9 1303 1453 535445619 535445784 6.130000e-12 82.4


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 TraesCS3B01G317500 chr3B 511070108 511072778 2670 False 4933.000000 4933 100.000000 1 2671 1 chr3B.!!$F1 2670
1 TraesCS3B01G317500 chr3D 392053194 392056177 2983 False 549.366667 1321 90.093333 1 2665 6 chr3D.!!$F1 2664
2 TraesCS3B01G317500 chr3A 512306760 512309922 3162 False 400.400000 1219 88.237571 1 2668 7 chr3A.!!$F1 2667

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
703 1161 0.179124 GGAGAAACTGATCGCTCGCT 60.179 55.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3001 0.038744 CTGGGCCTGAAACTCCACAT 59.961 55.0 4.53 0.0 0.0 3.21 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
127 139 3.236618 GACGCGTTGTGCCCAGTTC 62.237 63.158 15.53 0.00 42.08 3.01
133 145 3.808218 TTGTGCCCAGTTCCTGCCC 62.808 63.158 0.00 0.00 0.00 5.36
136 148 2.118294 GCCCAGTTCCTGCCCTTT 59.882 61.111 0.00 0.00 0.00 3.11
237 250 4.359706 GGCAATAACGAAACCAATGATCC 58.640 43.478 0.00 0.00 0.00 3.36
238 251 4.142271 GGCAATAACGAAACCAATGATCCA 60.142 41.667 0.00 0.00 0.00 3.41
239 252 4.798387 GCAATAACGAAACCAATGATCCAC 59.202 41.667 0.00 0.00 0.00 4.02
240 253 5.393027 GCAATAACGAAACCAATGATCCACT 60.393 40.000 0.00 0.00 0.00 4.00
241 254 6.258160 CAATAACGAAACCAATGATCCACTC 58.742 40.000 0.00 0.00 0.00 3.51
242 255 2.346803 ACGAAACCAATGATCCACTCG 58.653 47.619 0.00 0.00 0.00 4.18
243 256 2.028476 ACGAAACCAATGATCCACTCGA 60.028 45.455 0.00 0.00 0.00 4.04
257 270 2.421073 CCACTCGACACTCGTAATGGTA 59.579 50.000 0.00 0.00 41.35 3.25
258 271 3.423571 CACTCGACACTCGTAATGGTAC 58.576 50.000 0.00 0.00 41.35 3.34
389 406 0.612229 ACGAGTAGGTCCGTGAGAGA 59.388 55.000 0.00 0.00 37.64 3.10
400 417 1.979693 GTGAGAGAGTCGCAGGGGT 60.980 63.158 0.00 0.00 35.56 4.95
418 435 4.760047 GCAGGGGACGCGTGTGAT 62.760 66.667 20.70 0.00 0.00 3.06
504 521 2.582498 GCGCTCGTGTATTCGGCT 60.582 61.111 0.00 0.00 0.00 5.52
546 563 2.480419 GCGCGGTGCTTTAGATAATGAT 59.520 45.455 8.83 0.00 41.73 2.45
547 564 3.678072 GCGCGGTGCTTTAGATAATGATA 59.322 43.478 8.83 0.00 41.73 2.15
548 565 4.201628 GCGCGGTGCTTTAGATAATGATAG 60.202 45.833 8.83 0.00 41.73 2.08
572 741 8.040716 AGTATAACTTTCAAAGGATTTCACCG 57.959 34.615 1.31 0.00 35.03 4.94
577 746 3.426787 TCAAAGGATTTCACCGCCTTA 57.573 42.857 0.00 0.00 40.97 2.69
642 811 1.577328 CGTCACCTGCCACCAATGAC 61.577 60.000 0.00 0.00 35.40 3.06
661 830 4.883083 TGACCGGATTCATGATTAGTAGC 58.117 43.478 9.46 0.00 0.00 3.58
665 1123 5.527582 ACCGGATTCATGATTAGTAGCAAAC 59.472 40.000 9.46 0.00 0.00 2.93
703 1161 0.179124 GGAGAAACTGATCGCTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
717 1175 3.120752 TCGCTCGCTCTTGTATATACGAC 60.121 47.826 8.33 0.00 0.00 4.34
718 1176 3.490399 GCTCGCTCTTGTATATACGACC 58.510 50.000 8.33 0.00 0.00 4.79
719 1177 3.058432 GCTCGCTCTTGTATATACGACCA 60.058 47.826 8.33 0.00 0.00 4.02
720 1178 4.556104 GCTCGCTCTTGTATATACGACCAA 60.556 45.833 8.33 0.00 0.00 3.67
723 1181 5.975344 TCGCTCTTGTATATACGACCAAAAG 59.025 40.000 8.33 5.44 0.00 2.27
741 1200 5.182760 CCAAAAGTAGATTGCAGCTTCTTCT 59.817 40.000 9.74 2.44 0.00 2.85
745 1204 6.890979 AGTAGATTGCAGCTTCTTCTTTTT 57.109 33.333 4.08 0.00 0.00 1.94
746 1205 7.986085 AGTAGATTGCAGCTTCTTCTTTTTA 57.014 32.000 4.08 0.00 0.00 1.52
747 1206 8.396272 AGTAGATTGCAGCTTCTTCTTTTTAA 57.604 30.769 4.08 0.00 0.00 1.52
748 1207 9.018582 AGTAGATTGCAGCTTCTTCTTTTTAAT 57.981 29.630 4.08 0.00 0.00 1.40
788 1247 0.798776 CAGCTTCATGTCGACCAACC 59.201 55.000 14.12 0.00 0.00 3.77
799 1258 6.761242 TCATGTCGACCAACCTTATTTCTATG 59.239 38.462 14.12 4.83 0.00 2.23
946 1408 0.892755 TGGGAAGCTACACCTACACG 59.107 55.000 0.00 0.00 0.00 4.49
1009 1471 3.445857 GTCACAGGATAGGACGCTAAAC 58.554 50.000 0.00 0.00 0.00 2.01
1050 1512 2.026449 AGCTTCCAATCCAAGTCCTCAG 60.026 50.000 0.00 0.00 0.00 3.35
1053 1515 1.909302 TCCAATCCAAGTCCTCAGTCC 59.091 52.381 0.00 0.00 0.00 3.85
1059 1521 1.342074 CAAGTCCTCAGTCCTCACCA 58.658 55.000 0.00 0.00 0.00 4.17
1092 1554 1.063327 CGAGCACAAAACCGCACAA 59.937 52.632 0.00 0.00 0.00 3.33
1226 1688 2.110213 GACCACCGGCAGTGTTCA 59.890 61.111 0.00 0.00 45.74 3.18
1241 1703 2.651105 TTCAGCGCCGGTGGACATA 61.651 57.895 18.41 0.00 0.00 2.29
1245 1707 4.540735 CGCCGGTGGACATACCCC 62.541 72.222 7.26 0.00 37.44 4.95
1247 1709 3.078836 CCGGTGGACATACCCCGT 61.079 66.667 0.00 0.00 44.86 5.28
1249 1711 2.587889 GGTGGACATACCCCGTGG 59.412 66.667 0.00 0.00 38.00 4.94
1251 1713 3.404438 TGGACATACCCCGTGGCC 61.404 66.667 0.00 0.00 45.44 5.36
1252 1714 4.540735 GGACATACCCCGTGGCCG 62.541 72.222 0.00 0.00 34.49 6.13
1253 1715 3.777910 GACATACCCCGTGGCCGT 61.778 66.667 0.00 0.00 33.59 5.68
1510 1987 1.772063 AAAAGTCAGTCACCACGCGC 61.772 55.000 5.73 0.00 0.00 6.86
1517 1994 4.373116 TCACCACGCGCCTTCTCC 62.373 66.667 5.73 0.00 0.00 3.71
1549 2026 2.574322 CAGTCAATTTTGTTCGGCTCG 58.426 47.619 0.00 0.00 0.00 5.03
1555 2032 2.234300 TTTTGTTCGGCTCGTCTTCT 57.766 45.000 0.00 0.00 0.00 2.85
1561 2038 2.963371 GGCTCGTCTTCTCCGTGT 59.037 61.111 0.00 0.00 0.00 4.49
1581 2058 8.037758 TCCGTGTTTGCCAATCAAATTAATTAT 58.962 29.630 0.01 0.00 45.43 1.28
1627 2105 5.125367 TCAGCCAGTAGTGAGTTAGGATA 57.875 43.478 0.00 0.00 0.00 2.59
1629 2107 6.136857 TCAGCCAGTAGTGAGTTAGGATATT 58.863 40.000 0.00 0.00 0.00 1.28
1630 2108 6.611642 TCAGCCAGTAGTGAGTTAGGATATTT 59.388 38.462 0.00 0.00 0.00 1.40
1631 2109 7.125811 TCAGCCAGTAGTGAGTTAGGATATTTT 59.874 37.037 0.00 0.00 0.00 1.82
1632 2110 8.421784 CAGCCAGTAGTGAGTTAGGATATTTTA 58.578 37.037 0.00 0.00 0.00 1.52
1633 2111 9.160412 AGCCAGTAGTGAGTTAGGATATTTTAT 57.840 33.333 0.00 0.00 0.00 1.40
1634 2112 9.780186 GCCAGTAGTGAGTTAGGATATTTTATT 57.220 33.333 0.00 0.00 0.00 1.40
1657 2135 7.883229 TTTTTCTTTTCGGAATGGAATAAGC 57.117 32.000 0.00 0.00 0.00 3.09
1670 2156 6.903883 ATGGAATAAGCTACGTTTGTACTG 57.096 37.500 0.00 0.00 0.00 2.74
1725 2352 1.195115 TTCATCCTTGGTCCGGAGAG 58.805 55.000 3.06 3.06 33.29 3.20
1778 2405 5.511202 GGCTTTTGATCAATCCTGTGGAAAA 60.511 40.000 9.40 0.00 34.34 2.29
1779 2406 5.990996 GCTTTTGATCAATCCTGTGGAAAAA 59.009 36.000 9.40 0.00 34.34 1.94
1811 2439 1.000938 GACAAAACAGAGCAAGCCTGG 60.001 52.381 12.79 0.00 36.03 4.45
1887 2529 9.146270 CAAAAATGCTAAAGAAAACATCAAACG 57.854 29.630 0.00 0.00 0.00 3.60
1896 2538 4.338118 AGAAAACATCAAACGAGGCTTCAA 59.662 37.500 0.00 0.00 0.00 2.69
1903 2545 1.226746 AACGAGGCTTCAAGGAAACG 58.773 50.000 0.00 0.00 0.00 3.60
1906 2548 0.960861 GAGGCTTCAAGGAAACGGGG 60.961 60.000 0.00 0.00 0.00 5.73
1929 2571 5.376854 AACAGTTTGTATGGAATGAGCAC 57.623 39.130 0.00 0.00 0.00 4.40
1942 2584 6.314917 TGGAATGAGCACCTATCATCTACTA 58.685 40.000 0.00 0.00 36.38 1.82
1943 2585 6.435591 TGGAATGAGCACCTATCATCTACTAG 59.564 42.308 0.00 0.00 36.38 2.57
1944 2586 6.661377 GGAATGAGCACCTATCATCTACTAGA 59.339 42.308 0.00 0.00 36.38 2.43
1945 2587 7.362574 GGAATGAGCACCTATCATCTACTAGAC 60.363 44.444 0.00 0.00 36.38 2.59
1946 2588 4.998033 TGAGCACCTATCATCTACTAGACG 59.002 45.833 0.00 0.00 0.00 4.18
1947 2589 4.328536 AGCACCTATCATCTACTAGACGG 58.671 47.826 0.00 0.00 0.00 4.79
1948 2590 4.073549 GCACCTATCATCTACTAGACGGT 58.926 47.826 0.00 0.00 0.00 4.83
1949 2591 5.012871 AGCACCTATCATCTACTAGACGGTA 59.987 44.000 0.00 0.00 0.00 4.02
1975 2744 0.165944 GCACGAAAAGGTCCATGACG 59.834 55.000 0.00 0.00 32.65 4.35
2072 2891 8.259049 TGATGGTTTTACCGTTAATACTCTTG 57.741 34.615 0.00 0.00 42.58 3.02
2083 2902 7.497909 ACCGTTAATACTCTTGGTTATTGATGG 59.502 37.037 0.00 0.00 33.45 3.51
2098 2917 1.344458 GATGGCACTCATCTATCGCG 58.656 55.000 0.00 0.00 46.59 5.87
2127 2947 4.818546 ACAAATAGCTGCATACAGGATGAC 59.181 41.667 1.02 0.00 44.63 3.06
2130 2950 3.123157 AGCTGCATACAGGATGACATC 57.877 47.619 6.91 6.91 44.63 3.06
2166 2986 1.512926 CTCGGCAAGCAAACTACTGT 58.487 50.000 0.00 0.00 0.00 3.55
2167 2987 2.683968 CTCGGCAAGCAAACTACTGTA 58.316 47.619 0.00 0.00 0.00 2.74
2176 2996 6.659776 CAAGCAAACTACTGTAGAAGGAAAC 58.340 40.000 21.01 4.33 0.00 2.78
2177 2997 4.989168 AGCAAACTACTGTAGAAGGAAACG 59.011 41.667 21.01 2.57 0.00 3.60
2178 2998 4.986659 GCAAACTACTGTAGAAGGAAACGA 59.013 41.667 21.01 0.00 0.00 3.85
2179 2999 5.118817 GCAAACTACTGTAGAAGGAAACGAG 59.881 44.000 21.01 0.00 0.00 4.18
2180 3000 4.437772 ACTACTGTAGAAGGAAACGAGC 57.562 45.455 21.01 0.00 0.00 5.03
2181 3001 3.825014 ACTACTGTAGAAGGAAACGAGCA 59.175 43.478 21.01 0.00 0.00 4.26
2182 3002 3.963428 ACTGTAGAAGGAAACGAGCAT 57.037 42.857 0.00 0.00 0.00 3.79
2183 3003 3.589988 ACTGTAGAAGGAAACGAGCATG 58.410 45.455 0.00 0.00 0.00 4.06
2188 3008 1.734465 GAAGGAAACGAGCATGTGGAG 59.266 52.381 0.00 0.00 0.00 3.86
2192 3012 2.095718 GGAAACGAGCATGTGGAGTTTC 60.096 50.000 19.86 19.86 45.65 2.78
2208 3028 2.673775 TTTCAGGCCCAGAAACATCA 57.326 45.000 15.00 0.00 30.56 3.07
2209 3029 2.905415 TTCAGGCCCAGAAACATCAT 57.095 45.000 0.00 0.00 0.00 2.45
2210 3030 2.425143 TCAGGCCCAGAAACATCATC 57.575 50.000 0.00 0.00 0.00 2.92
2229 3054 4.214119 TCATCTGAAAGCCGAAAGACAAAG 59.786 41.667 0.00 0.00 0.00 2.77
2233 3058 1.388547 AAGCCGAAAGACAAAGTGCA 58.611 45.000 0.00 0.00 0.00 4.57
2246 3071 3.047796 CAAAGTGCAGAAATCACAGTGC 58.952 45.455 0.00 0.00 36.93 4.40
2265 3090 0.250209 CCCTCATCGCCTTGATCCAG 60.250 60.000 0.00 0.00 34.13 3.86
2312 3137 1.561542 CCCAGTCTTAGCACCAGGAAT 59.438 52.381 0.00 0.00 0.00 3.01
2328 3153 3.518003 ATGCCGCCTTCTGCATTC 58.482 55.556 0.00 0.00 45.52 2.67
2487 3472 1.472480 ACATAATTGCCAGTTGCGACC 59.528 47.619 0.00 0.00 45.60 4.79
2491 3476 0.537143 ATTGCCAGTTGCGACCAGAA 60.537 50.000 0.00 0.00 45.60 3.02
2494 3479 0.598065 GCCAGTTGCGACCAGAAAAT 59.402 50.000 0.00 0.00 0.00 1.82
2668 3653 9.817365 CAATTATTCATTATCTTTGCTAGTCGG 57.183 33.333 0.00 0.00 0.00 4.79
2669 3654 9.778741 AATTATTCATTATCTTTGCTAGTCGGA 57.221 29.630 0.00 0.00 0.00 4.55
2670 3655 9.950496 ATTATTCATTATCTTTGCTAGTCGGAT 57.050 29.630 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 64 3.377798 GCCCAATCCGTCCGTTATTTTAA 59.622 43.478 0.00 0.00 0.00 1.52
61 66 1.746787 GCCCAATCCGTCCGTTATTTT 59.253 47.619 0.00 0.00 0.00 1.82
140 152 0.389817 CGCGTGTCTGATCCAGGAAA 60.390 55.000 0.00 0.00 31.51 3.13
141 153 1.215382 CGCGTGTCTGATCCAGGAA 59.785 57.895 0.00 0.00 31.51 3.36
142 154 1.934220 GACGCGTGTCTGATCCAGGA 61.934 60.000 20.70 0.00 42.08 3.86
143 155 1.517257 GACGCGTGTCTGATCCAGG 60.517 63.158 20.70 0.00 42.08 4.45
144 156 1.869574 CGACGCGTGTCTGATCCAG 60.870 63.158 25.28 5.60 43.21 3.86
146 158 1.583967 CTCGACGCGTGTCTGATCC 60.584 63.158 25.28 0.00 43.21 3.36
147 159 2.218239 GCTCGACGCGTGTCTGATC 61.218 63.158 25.28 15.72 43.21 2.92
182 194 2.027385 GGCAAGCTAAAGGATGGGAAG 58.973 52.381 0.00 0.00 0.00 3.46
221 234 2.742053 CGAGTGGATCATTGGTTTCGTT 59.258 45.455 0.00 0.00 0.00 3.85
237 250 2.631418 ACCATTACGAGTGTCGAGTG 57.369 50.000 2.82 0.00 43.74 3.51
238 251 3.754188 GTACCATTACGAGTGTCGAGT 57.246 47.619 2.82 0.00 43.74 4.18
257 270 4.657824 CGGACCGGTTGCAGTCGT 62.658 66.667 9.42 0.00 33.66 4.34
258 271 3.642778 ATCGGACCGGTTGCAGTCG 62.643 63.158 15.25 6.80 33.66 4.18
303 319 2.111756 GCGCTTTGCTAATCATTTCGG 58.888 47.619 0.00 0.00 41.73 4.30
358 375 2.688958 ACCTACTCGTGTAATCTCTGGC 59.311 50.000 0.00 0.00 0.00 4.85
362 379 2.941720 ACGGACCTACTCGTGTAATCTC 59.058 50.000 0.00 0.00 38.25 2.75
418 435 5.991606 CCAGATTAATTAATCCTCGACTGCA 59.008 40.000 27.18 0.00 42.29 4.41
421 438 8.195165 TGATCCAGATTAATTAATCCTCGACT 57.805 34.615 27.18 10.88 42.29 4.18
504 521 1.090728 CAGCAGCTCTGACGAGACTA 58.909 55.000 7.22 0.00 45.72 2.59
546 563 9.158233 CGGTGAAATCCTTTGAAAGTTATACTA 57.842 33.333 4.02 0.00 0.00 1.82
547 564 7.361799 GCGGTGAAATCCTTTGAAAGTTATACT 60.362 37.037 4.02 0.00 0.00 2.12
548 565 6.745907 GCGGTGAAATCCTTTGAAAGTTATAC 59.254 38.462 4.02 0.00 0.00 1.47
596 765 3.134623 TGCCACATACACCTTCAGATAGG 59.865 47.826 0.00 0.00 41.31 2.57
642 811 5.333339 CGTTTGCTACTAATCATGAATCCGG 60.333 44.000 0.00 0.00 0.00 5.14
661 830 6.430000 TCCCTCTATTTTCTTTCTTCCGTTTG 59.570 38.462 0.00 0.00 0.00 2.93
665 1123 5.978814 TCTCCCTCTATTTTCTTTCTTCCG 58.021 41.667 0.00 0.00 0.00 4.30
717 1175 5.182760 AGAAGAAGCTGCAATCTACTTTTGG 59.817 40.000 1.02 0.00 0.00 3.28
718 1176 6.251655 AGAAGAAGCTGCAATCTACTTTTG 57.748 37.500 1.02 0.00 0.00 2.44
719 1177 6.890979 AAGAAGAAGCTGCAATCTACTTTT 57.109 33.333 1.02 0.00 0.00 2.27
720 1178 6.890979 AAAGAAGAAGCTGCAATCTACTTT 57.109 33.333 1.02 3.96 0.00 2.66
808 1267 9.950680 CACACACATAGAAATAAAGTTGTTTCT 57.049 29.630 16.71 16.71 46.09 2.52
809 1268 9.944663 TCACACACATAGAAATAAAGTTGTTTC 57.055 29.630 5.42 5.42 38.20 2.78
810 1269 9.950680 CTCACACACATAGAAATAAAGTTGTTT 57.049 29.630 0.00 0.00 0.00 2.83
811 1270 8.076178 GCTCACACACATAGAAATAAAGTTGTT 58.924 33.333 0.00 0.00 0.00 2.83
812 1271 7.308589 GGCTCACACACATAGAAATAAAGTTGT 60.309 37.037 0.00 0.00 0.00 3.32
813 1272 7.023575 GGCTCACACACATAGAAATAAAGTTG 58.976 38.462 0.00 0.00 0.00 3.16
814 1273 6.128282 CGGCTCACACACATAGAAATAAAGTT 60.128 38.462 0.00 0.00 0.00 2.66
825 1284 1.188871 TCCACCGGCTCACACACATA 61.189 55.000 0.00 0.00 0.00 2.29
826 1285 1.841302 ATCCACCGGCTCACACACAT 61.841 55.000 0.00 0.00 0.00 3.21
827 1286 2.050836 AATCCACCGGCTCACACACA 62.051 55.000 0.00 0.00 0.00 3.72
1009 1471 4.874966 AGCTCGATGATCTTTCTTTTCTGG 59.125 41.667 0.00 0.00 0.00 3.86
1050 1512 1.337823 ACGTATTGCACTGGTGAGGAC 60.338 52.381 4.79 0.00 0.00 3.85
1092 1554 1.681793 CTCCTCCACCGTCGACATATT 59.318 52.381 17.16 0.00 0.00 1.28
1223 1685 2.651105 TATGTCCACCGGCGCTGAA 61.651 57.895 20.25 0.00 0.00 3.02
1226 1688 4.157120 GGTATGTCCACCGGCGCT 62.157 66.667 7.64 0.00 35.97 5.92
1510 1987 1.966451 GCCAACACCGTGGAGAAGG 60.966 63.158 3.03 0.00 41.65 3.46
1517 1994 1.172180 ATTGACTGGCCAACACCGTG 61.172 55.000 7.01 0.00 0.00 4.94
1549 2026 1.305201 TTGGCAAACACGGAGAAGAC 58.695 50.000 0.00 0.00 0.00 3.01
1581 2058 4.853468 TGCATCAACCAAGGGATACTAA 57.147 40.909 0.00 0.00 0.00 2.24
1583 2060 3.737559 TTGCATCAACCAAGGGATACT 57.262 42.857 0.00 0.00 0.00 2.12
1584 2061 4.402155 TGATTTGCATCAACCAAGGGATAC 59.598 41.667 0.00 0.00 36.41 2.24
1585 2062 4.608269 TGATTTGCATCAACCAAGGGATA 58.392 39.130 0.00 0.00 36.41 2.59
1631 2109 9.581099 GCTTATTCCATTCCGAAAAGAAAAATA 57.419 29.630 1.56 0.00 0.00 1.40
1632 2110 8.314021 AGCTTATTCCATTCCGAAAAGAAAAAT 58.686 29.630 1.56 0.00 0.00 1.82
1633 2111 7.666623 AGCTTATTCCATTCCGAAAAGAAAAA 58.333 30.769 1.56 0.00 0.00 1.94
1634 2112 7.227049 AGCTTATTCCATTCCGAAAAGAAAA 57.773 32.000 1.56 0.00 0.00 2.29
1638 2116 5.293569 ACGTAGCTTATTCCATTCCGAAAAG 59.706 40.000 0.00 0.00 0.00 2.27
1657 2135 7.197017 AGAATCTCATAGCAGTACAAACGTAG 58.803 38.462 0.00 0.00 0.00 3.51
1670 2156 6.073873 CGGTTCAATCTGAAGAATCTCATAGC 60.074 42.308 5.37 0.00 37.00 2.97
1715 2342 0.685660 AACAGAAACCTCTCCGGACC 59.314 55.000 0.00 0.00 36.31 4.46
1725 2352 4.922791 GCGACAGCAACAGAAACC 57.077 55.556 0.00 0.00 44.35 3.27
1794 2422 2.508526 CTACCAGGCTTGCTCTGTTTT 58.491 47.619 0.00 0.00 0.00 2.43
1811 2439 1.089920 TGCTCGGTACTTCGACCTAC 58.910 55.000 0.00 0.00 37.34 3.18
1883 2525 1.602377 CGTTTCCTTGAAGCCTCGTTT 59.398 47.619 0.00 0.00 0.00 3.60
1887 2529 0.960861 CCCCGTTTCCTTGAAGCCTC 60.961 60.000 0.00 0.00 0.00 4.70
1896 2538 1.064240 ACAAACTGTTCCCCGTTTCCT 60.064 47.619 0.00 0.00 31.46 3.36
1903 2545 4.340617 TCATTCCATACAAACTGTTCCCC 58.659 43.478 0.00 0.00 0.00 4.81
1906 2548 5.393962 GTGCTCATTCCATACAAACTGTTC 58.606 41.667 0.00 0.00 0.00 3.18
1918 2560 5.150715 AGTAGATGATAGGTGCTCATTCCA 58.849 41.667 0.00 0.00 33.56 3.53
1919 2561 5.736951 AGTAGATGATAGGTGCTCATTCC 57.263 43.478 0.00 0.00 33.56 3.01
1929 2571 5.350914 CCGTTACCGTCTAGTAGATGATAGG 59.649 48.000 19.20 12.18 33.07 2.57
1942 2584 0.955428 TCGTGCTACCGTTACCGTCT 60.955 55.000 0.00 0.00 0.00 4.18
1943 2585 0.109781 TTCGTGCTACCGTTACCGTC 60.110 55.000 0.00 0.00 0.00 4.79
1944 2586 0.313672 TTTCGTGCTACCGTTACCGT 59.686 50.000 0.00 0.00 0.00 4.83
1945 2587 1.387756 CTTTTCGTGCTACCGTTACCG 59.612 52.381 0.00 0.00 0.00 4.02
1946 2588 1.728425 CCTTTTCGTGCTACCGTTACC 59.272 52.381 0.00 0.00 0.00 2.85
1947 2589 2.407090 ACCTTTTCGTGCTACCGTTAC 58.593 47.619 0.00 0.00 0.00 2.50
1948 2590 2.610232 GGACCTTTTCGTGCTACCGTTA 60.610 50.000 0.00 0.00 0.00 3.18
1949 2591 1.505425 GACCTTTTCGTGCTACCGTT 58.495 50.000 0.00 0.00 0.00 4.44
2064 2883 6.006275 AGTGCCATCAATAACCAAGAGTAT 57.994 37.500 0.00 0.00 0.00 2.12
2083 2902 1.401670 CCTACCGCGATAGATGAGTGC 60.402 57.143 9.73 0.00 39.76 4.40
2098 2917 4.703897 TGTATGCAGCTATTTGTCCTACC 58.296 43.478 0.00 0.00 0.00 3.18
2127 2947 3.683802 AGCTCCTTCACAAAAGAGGATG 58.316 45.455 0.00 0.00 0.00 3.51
2130 2950 2.072298 CGAGCTCCTTCACAAAAGAGG 58.928 52.381 8.47 0.00 0.00 3.69
2162 2982 3.006967 ACATGCTCGTTTCCTTCTACAGT 59.993 43.478 0.00 0.00 0.00 3.55
2163 2983 3.369147 CACATGCTCGTTTCCTTCTACAG 59.631 47.826 0.00 0.00 0.00 2.74
2164 2984 3.325870 CACATGCTCGTTTCCTTCTACA 58.674 45.455 0.00 0.00 0.00 2.74
2165 2985 2.673368 CCACATGCTCGTTTCCTTCTAC 59.327 50.000 0.00 0.00 0.00 2.59
2166 2986 2.565391 TCCACATGCTCGTTTCCTTCTA 59.435 45.455 0.00 0.00 0.00 2.10
2167 2987 1.347707 TCCACATGCTCGTTTCCTTCT 59.652 47.619 0.00 0.00 0.00 2.85
2176 2996 1.081892 CCTGAAACTCCACATGCTCG 58.918 55.000 0.00 0.00 0.00 5.03
2177 2997 0.807496 GCCTGAAACTCCACATGCTC 59.193 55.000 0.00 0.00 0.00 4.26
2178 2998 0.610232 GGCCTGAAACTCCACATGCT 60.610 55.000 0.00 0.00 0.00 3.79
2179 2999 1.598701 GGGCCTGAAACTCCACATGC 61.599 60.000 0.84 0.00 0.00 4.06
2180 3000 0.251297 TGGGCCTGAAACTCCACATG 60.251 55.000 4.53 0.00 0.00 3.21
2181 3001 0.038744 CTGGGCCTGAAACTCCACAT 59.961 55.000 4.53 0.00 0.00 3.21
2182 3002 1.059584 TCTGGGCCTGAAACTCCACA 61.060 55.000 11.07 0.00 0.00 4.17
2183 3003 0.110486 TTCTGGGCCTGAAACTCCAC 59.890 55.000 21.86 0.00 0.00 4.02
2188 3008 2.238521 TGATGTTTCTGGGCCTGAAAC 58.761 47.619 40.12 40.12 45.71 2.78
2192 3012 2.022195 CAGATGATGTTTCTGGGCCTG 58.978 52.381 4.53 4.06 37.53 4.85
2208 3028 4.023707 CACTTTGTCTTTCGGCTTTCAGAT 60.024 41.667 0.00 0.00 0.00 2.90
2209 3029 3.312421 CACTTTGTCTTTCGGCTTTCAGA 59.688 43.478 0.00 0.00 0.00 3.27
2210 3030 3.621794 CACTTTGTCTTTCGGCTTTCAG 58.378 45.455 0.00 0.00 0.00 3.02
2229 3054 0.242017 GGGCACTGTGATTTCTGCAC 59.758 55.000 12.86 0.00 36.81 4.57
2233 3058 2.679059 CGATGAGGGCACTGTGATTTCT 60.679 50.000 12.86 2.32 0.00 2.52
2246 3071 0.250209 CTGGATCAAGGCGATGAGGG 60.250 60.000 0.00 0.00 33.17 4.30
2265 3090 5.519206 AGGCGATTTTAGATTAGACGTTGAC 59.481 40.000 0.00 0.00 0.00 3.18
2328 3153 2.611518 GTGGGAATGTCTCTCTCGTTG 58.388 52.381 0.00 0.00 0.00 4.10
2487 3472 6.030228 GCGAATCCTGAAGGTAAATTTTCTG 58.970 40.000 0.00 0.00 36.34 3.02
2491 3476 4.340617 TGGCGAATCCTGAAGGTAAATTT 58.659 39.130 0.00 0.00 36.34 1.82
2494 3479 2.939640 GCTGGCGAATCCTGAAGGTAAA 60.940 50.000 0.00 0.00 35.98 2.01
2618 3603 4.000325 TGTCCAGTCAACATAATGTTCCG 59.000 43.478 0.00 0.00 38.77 4.30


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

AutoCloner maintained by Alex Coulton.