Multiple sequence alignment - TraesCS7B01G385700

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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 TraesCS7B01G385700 chr7B 100.000 4872 0 0 1 4872 650615129 650610258 0.000000e+00 8997.0
1 TraesCS7B01G385700 chr7D 93.535 3960 134 36 124 4031 583067386 583063497 0.000000e+00 5782.0
2 TraesCS7B01G385700 chr7D 92.099 848 46 6 4028 4872 583063197 583062368 0.000000e+00 1175.0
3 TraesCS7B01G385700 chr7D 92.982 114 8 0 1 114 583067482 583067369 3.020000e-37 167.0
4 TraesCS7B01G385700 chr7D 97.500 40 1 0 4061 4100 583063197 583063158 8.750000e-08 69.4
5 TraesCS7B01G385700 chr7A 90.825 2267 128 40 1 2217 674817836 674815600 0.000000e+00 2961.0
6 TraesCS7B01G385700 chr7A 95.852 1832 50 12 2247 4067 674815606 674813790 0.000000e+00 2939.0
7 TraesCS7B01G385700 chr7A 89.320 824 67 7 4053 4872 674813837 674813031 0.000000e+00 1014.0
8 TraesCS7B01G385700 chr6D 77.972 286 47 12 1335 1613 115772127 115772403 1.080000e-36 165.0
9 TraesCS7B01G385700 chr6B 77.895 285 47 12 1335 1613 205234733 205235007 3.900000e-36 163.0
10 TraesCS7B01G385700 chr6A 78.049 287 44 14 1335 1613 144247521 144247796 3.900000e-36 163.0
11 TraesCS7B01G385700 chr2A 93.878 49 3 0 1569 1617 24909547 24909595 1.880000e-09 75.0
12 TraesCS7B01G385700 chr2A 92.453 53 2 1 1572 1624 25099422 25099372 1.880000e-09 75.0


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 TraesCS7B01G385700 chr7B 650610258 650615129 4871 True 8997.000000 8997 100.000 1 4872 1 chr7B.!!$R1 4871
1 TraesCS7B01G385700 chr7D 583062368 583067482 5114 True 1798.350000 5782 94.029 1 4872 4 chr7D.!!$R1 4871
2 TraesCS7B01G385700 chr7A 674813031 674817836 4805 True 2304.666667 2961 91.999 1 4872 3 chr7A.!!$R1 4871

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
435 444 1.659098 CCGTGTGTTCGAAAGCCTATC 59.341 52.381 0.00 0.00 0.00 2.08 F
1061 1116 0.400213 CAGCCAAGGGAAGTACCACA 59.600 55.000 0.00 0.00 41.20 4.17 F
2798 2891 0.388778 TTGCATTGCAATGACGCCAG 60.389 50.000 37.36 14.12 43.99 4.85 F
3087 3180 0.471780 TGAGCTTCCAGGACCTCACA 60.472 55.000 12.96 0.00 30.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2194 0.405198 TGCTGCAGGGAATTTGGAGA 59.595 50.0 17.12 0.0 36.24 3.71 R
2805 2898 0.109153 CTGGATGGGATCGATGGCAA 59.891 55.0 0.54 0.0 0.00 4.52 R
3610 3704 0.103208 CTTAGCTACACCTCAGCCCG 59.897 60.0 0.00 0.0 39.99 6.13 R
4586 5014 0.606604 AAACCGACGGCATGACTACT 59.393 50.0 15.39 0.0 0.00 2.57 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
51 52 2.027100 GGAAGGTGTTTGCCTAGCTAGT 60.027 50.000 19.31 0.00 38.03 2.57
63 64 3.772387 CCTAGCTAGTCTGGATGGATGA 58.228 50.000 19.31 0.00 0.00 2.92
65 66 3.037851 AGCTAGTCTGGATGGATGACA 57.962 47.619 0.00 0.00 33.56 3.58
81 82 5.363868 TGGATGACAGTCTAATCTCCGAATT 59.636 40.000 1.31 0.00 0.00 2.17
123 124 3.316868 TGTTTTCCTTGTCCCGCTAAAAG 59.683 43.478 0.00 0.00 0.00 2.27
127 128 4.028993 TCCTTGTCCCGCTAAAAGAAAT 57.971 40.909 0.00 0.00 0.00 2.17
141 142 7.306574 CGCTAAAAGAAATTGTTTTCCTTGTCC 60.307 37.037 4.07 0.00 41.86 4.02
157 158 5.189145 TCCTTGTCCTGGGACTACTTTTATC 59.811 44.000 18.92 0.00 44.80 1.75
198 203 1.766494 TTGGCCATGTGCATCCTAAG 58.234 50.000 6.09 0.00 43.89 2.18
259 264 2.971997 GTATCGGCTCGATGCAACA 58.028 52.632 17.04 0.00 46.43 3.33
311 320 3.378112 AGAATGATTGCATTACACCACCG 59.622 43.478 0.00 0.00 44.47 4.94
396 405 6.314899 TGTGGATTATTGTATGGTGGTACA 57.685 37.500 0.00 0.00 32.99 2.90
416 425 5.941948 ACACACTAAGATGCAAGTTAACC 57.058 39.130 0.88 0.00 0.00 2.85
417 426 4.451096 ACACACTAAGATGCAAGTTAACCG 59.549 41.667 0.88 0.00 0.00 4.44
435 444 1.659098 CCGTGTGTTCGAAAGCCTATC 59.341 52.381 0.00 0.00 0.00 2.08
445 454 2.287308 CGAAAGCCTATCGTCTCCAGAG 60.287 54.545 0.00 0.00 35.64 3.35
461 470 1.770658 CAGAGGATGTGGGAGCCATTA 59.229 52.381 0.00 0.00 35.28 1.90
462 471 2.374504 CAGAGGATGTGGGAGCCATTAT 59.625 50.000 0.00 0.00 35.28 1.28
467 476 3.760684 GGATGTGGGAGCCATTATGATTC 59.239 47.826 0.00 0.00 35.28 2.52
469 478 4.524802 TGTGGGAGCCATTATGATTCTT 57.475 40.909 0.00 0.00 35.28 2.52
473 482 6.126507 TGTGGGAGCCATTATGATTCTTAGAA 60.127 38.462 0.00 0.00 35.28 2.10
496 505 9.074576 AGAATGCAATCATCATCTTATAAAGCA 57.925 29.630 4.25 0.00 31.27 3.91
545 554 6.933514 TTCCATACATACAGATGAGCCATA 57.066 37.500 0.00 0.00 36.48 2.74
552 561 6.653020 ACATACAGATGAGCCATAAACTTCA 58.347 36.000 0.00 0.00 36.48 3.02
602 617 8.812329 GTTGTACTTAAATAGCATCTCACTCAG 58.188 37.037 0.00 0.00 0.00 3.35
630 646 5.819825 AACTGTCTGGAAAACACTCTTTC 57.180 39.130 0.00 0.00 35.04 2.62
637 653 5.408604 TCTGGAAAACACTCTTTCGATAAGC 59.591 40.000 0.00 0.00 36.37 3.09
665 681 4.704540 CACCCACAAGCAGATGGTATTAAA 59.295 41.667 0.00 0.00 33.80 1.52
803 819 7.099764 AGAAGCTTAGAGATGACAAAATTCGA 58.900 34.615 0.00 0.00 0.00 3.71
805 821 7.244166 AGCTTAGAGATGACAAAATTCGATG 57.756 36.000 0.00 0.00 0.00 3.84
818 834 5.720371 AAATTCGATGGTTGAATGGACAA 57.280 34.783 0.00 0.00 36.24 3.18
824 840 3.855255 TGGTTGAATGGACAACTCTCA 57.145 42.857 0.00 0.00 46.17 3.27
858 874 4.485208 GAAAAGAGGCGCGCGTCG 62.485 66.667 38.21 16.61 42.12 5.12
877 893 4.443266 GACAGCGGCGAGGCTTCT 62.443 66.667 12.98 0.00 42.53 2.85
1061 1116 0.400213 CAGCCAAGGGAAGTACCACA 59.600 55.000 0.00 0.00 41.20 4.17
1471 1526 2.083774 TCGACCCATTCATGCTTGTTC 58.916 47.619 0.00 0.00 0.00 3.18
1480 1535 1.699083 TCATGCTTGTTCCAGTCCAGA 59.301 47.619 0.00 0.00 0.00 3.86
1613 1668 4.155709 TCTCAAGAGTCATCTTCAGGTGT 58.844 43.478 0.00 0.00 44.15 4.16
1652 1707 9.634021 AGAATTAGGTTTTTGTTTCTCTCTCTT 57.366 29.630 0.00 0.00 0.00 2.85
1656 1711 7.561021 AGGTTTTTGTTTCTCTCTCTTTCTC 57.439 36.000 0.00 0.00 0.00 2.87
1657 1712 7.342581 AGGTTTTTGTTTCTCTCTCTTTCTCT 58.657 34.615 0.00 0.00 0.00 3.10
1658 1713 7.497579 AGGTTTTTGTTTCTCTCTCTTTCTCTC 59.502 37.037 0.00 0.00 0.00 3.20
1659 1714 7.497579 GGTTTTTGTTTCTCTCTCTTTCTCTCT 59.502 37.037 0.00 0.00 0.00 3.10
1660 1715 8.547894 GTTTTTGTTTCTCTCTCTTTCTCTCTC 58.452 37.037 0.00 0.00 0.00 3.20
1661 1716 5.975693 TGTTTCTCTCTCTTTCTCTCTCC 57.024 43.478 0.00 0.00 0.00 3.71
1662 1717 4.770010 TGTTTCTCTCTCTTTCTCTCTCCC 59.230 45.833 0.00 0.00 0.00 4.30
1663 1718 4.946160 TTCTCTCTCTTTCTCTCTCCCT 57.054 45.455 0.00 0.00 0.00 4.20
1664 1719 4.503714 TCTCTCTCTTTCTCTCTCCCTC 57.496 50.000 0.00 0.00 0.00 4.30
1665 1720 4.111577 TCTCTCTCTTTCTCTCTCCCTCT 58.888 47.826 0.00 0.00 0.00 3.69
1666 1721 4.164221 TCTCTCTCTTTCTCTCTCCCTCTC 59.836 50.000 0.00 0.00 0.00 3.20
1667 1722 4.111577 TCTCTCTTTCTCTCTCCCTCTCT 58.888 47.826 0.00 0.00 0.00 3.10
1668 1723 4.164221 TCTCTCTTTCTCTCTCCCTCTCTC 59.836 50.000 0.00 0.00 0.00 3.20
1669 1724 4.111577 TCTCTTTCTCTCTCCCTCTCTCT 58.888 47.826 0.00 0.00 0.00 3.10
1670 1725 4.164221 TCTCTTTCTCTCTCCCTCTCTCTC 59.836 50.000 0.00 0.00 0.00 3.20
1671 1726 4.111577 TCTTTCTCTCTCCCTCTCTCTCT 58.888 47.826 0.00 0.00 0.00 3.10
1672 1727 4.164221 TCTTTCTCTCTCCCTCTCTCTCTC 59.836 50.000 0.00 0.00 0.00 3.20
1673 1728 3.421394 TCTCTCTCCCTCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
1674 1729 3.309296 TCTCTCTCCCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1675 1730 3.051803 TCTCTCTCCCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1676 1731 3.309296 TCTCTCCCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1677 1732 2.370189 CTCTCCCTCTCTCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
1678 1733 1.421646 CTCCCTCTCTCTCTCTCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
1679 1734 0.478507 CCCTCTCTCTCTCTCTCCCC 59.521 65.000 0.00 0.00 0.00 4.81
1684 1753 1.852965 CTCTCTCTCTCTCCCCCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
1688 1757 2.657459 TCTCTCTCTCCCCCTCTTTCTT 59.343 50.000 0.00 0.00 0.00 2.52
1799 1868 4.069304 CACTCGGTCAAGGATGGTAAAAA 58.931 43.478 0.00 0.00 0.00 1.94
1834 1903 9.157104 TCTACTTGTTAAAAATCGATGTGCATA 57.843 29.630 0.00 0.00 0.00 3.14
1835 1904 9.935682 CTACTTGTTAAAAATCGATGTGCATAT 57.064 29.630 0.00 0.00 0.00 1.78
1908 1981 5.469760 TCACATATATGTTTGCATTCCCTCG 59.530 40.000 15.85 0.63 39.39 4.63
1947 2020 7.631717 AAACCTAGCTTATTCATCTGGAAAC 57.368 36.000 0.00 0.00 39.39 2.78
1958 2031 7.707624 ATTCATCTGGAAACATGTTACATGT 57.292 32.000 23.48 23.48 41.51 3.21
1959 2032 7.523293 TTCATCTGGAAACATGTTACATGTT 57.477 32.000 30.80 30.80 43.35 2.71
1960 2033 8.628630 TTCATCTGGAAACATGTTACATGTTA 57.371 30.769 34.48 23.01 40.94 2.41
1962 2035 7.882791 TCATCTGGAAACATGTTACATGTTAGT 59.117 33.333 34.48 24.17 40.94 2.24
1964 2037 6.007936 TGGAAACATGTTACATGTTAGTGC 57.992 37.500 34.48 26.79 40.94 4.40
1970 2051 6.003950 ACATGTTACATGTTAGTGCCTTTCT 58.996 36.000 23.48 0.00 0.00 2.52
2084 2165 8.373048 AGTAGTACTCGATCTCTTGTTCATAG 57.627 38.462 0.00 0.00 0.00 2.23
2085 2166 7.988599 AGTAGTACTCGATCTCTTGTTCATAGT 59.011 37.037 0.00 0.00 0.00 2.12
2092 2173 4.585955 TCTCTTGTTCATAGTATCGCCC 57.414 45.455 0.00 0.00 0.00 6.13
2093 2174 3.958147 TCTCTTGTTCATAGTATCGCCCA 59.042 43.478 0.00 0.00 0.00 5.36
2094 2175 4.038042 TCTCTTGTTCATAGTATCGCCCAG 59.962 45.833 0.00 0.00 0.00 4.45
2095 2176 3.069586 TCTTGTTCATAGTATCGCCCAGG 59.930 47.826 0.00 0.00 0.00 4.45
2096 2177 2.394632 TGTTCATAGTATCGCCCAGGT 58.605 47.619 0.00 0.00 0.00 4.00
2097 2178 2.769663 TGTTCATAGTATCGCCCAGGTT 59.230 45.455 0.00 0.00 0.00 3.50
2098 2179 3.962063 TGTTCATAGTATCGCCCAGGTTA 59.038 43.478 0.00 0.00 0.00 2.85
2099 2180 4.406326 TGTTCATAGTATCGCCCAGGTTAA 59.594 41.667 0.00 0.00 0.00 2.01
2110 2191 7.891498 ATCGCCCAGGTTAATTAATAAACTT 57.109 32.000 0.31 0.00 38.41 2.66
2112 2193 6.037391 TCGCCCAGGTTAATTAATAAACTTCG 59.963 38.462 0.31 1.67 38.41 3.79
2113 2194 6.183360 CGCCCAGGTTAATTAATAAACTTCGT 60.183 38.462 0.31 0.00 38.41 3.85
2116 2197 8.610035 CCCAGGTTAATTAATAAACTTCGTCTC 58.390 37.037 0.31 0.00 38.41 3.36
2798 2891 0.388778 TTGCATTGCAATGACGCCAG 60.389 50.000 37.36 14.12 43.99 4.85
2805 2898 1.750206 TGCAATGACGCCAGCATTATT 59.250 42.857 0.00 0.00 34.41 1.40
2821 2914 4.676196 GCATTATTTGCCATCGATCCCATC 60.676 45.833 0.00 0.00 46.15 3.51
2845 2938 3.960102 AGGTGCATTTTCACTTTCAAGGA 59.040 39.130 0.00 0.00 37.16 3.36
2952 3045 2.438021 GGGGAAGTACATGCAGTCCATA 59.562 50.000 0.00 0.00 31.47 2.74
3030 3123 1.249407 CCGGGTACAGATCTCTAGGC 58.751 60.000 0.00 0.00 0.00 3.93
3066 3159 3.764466 CTTGACCTCGGCGGCTCT 61.764 66.667 7.21 0.00 35.61 4.09
3087 3180 0.471780 TGAGCTTCCAGGACCTCACA 60.472 55.000 12.96 0.00 30.00 3.58
3093 3186 1.629043 TCCAGGACCTCACACTGTAC 58.371 55.000 0.00 0.00 0.00 2.90
3246 3339 1.152694 CCCGATGATGTGGGGCAAT 60.153 57.895 0.00 0.00 39.19 3.56
3580 3674 8.081633 CCTGTTGTCATGAAACAAGCTTAATTA 58.918 33.333 17.98 0.00 39.69 1.40
3610 3704 9.495754 CTTTTGCTAAGATCACTAAATAAGCAC 57.504 33.333 0.00 0.00 38.36 4.40
3672 3766 2.082140 ATGCTGATGATGCCCAATGT 57.918 45.000 0.00 0.00 0.00 2.71
3673 3767 1.855295 TGCTGATGATGCCCAATGTT 58.145 45.000 0.00 0.00 0.00 2.71
3747 3842 3.698040 TGGCGTTGGTTTAAGGTTTGTAA 59.302 39.130 0.00 0.00 0.00 2.41
3825 3925 6.942532 ATTCTTGTTCGGTGCATGTATTAT 57.057 33.333 0.00 0.00 0.00 1.28
3826 3926 8.445275 AATTCTTGTTCGGTGCATGTATTATA 57.555 30.769 0.00 0.00 0.00 0.98
3922 4030 6.038271 GTGTTCTCTGGTGTTATGTTTGAGTT 59.962 38.462 0.00 0.00 0.00 3.01
4024 4132 9.976511 ACATATTAATTTTGATCCTCTGCAATG 57.023 29.630 0.00 0.00 0.00 2.82
4101 4512 9.945904 AGGAAATTAAGCAGCCTTAGTATATAC 57.054 33.333 4.60 4.60 35.13 1.47
4234 4646 7.255242 CCATATGGATCGCTTCATAAACACTTT 60.255 37.037 17.49 0.00 37.39 2.66
4291 4703 5.389520 TCATTGGTTTGGTTCACCTAATCA 58.610 37.500 2.37 2.37 39.46 2.57
4294 4706 5.975693 TGGTTTGGTTCACCTAATCAATC 57.024 39.130 3.90 0.00 38.55 2.67
4406 4834 8.731275 TCACATTATCAATTTCTTACACGGAT 57.269 30.769 0.00 0.00 0.00 4.18
4407 4835 8.611757 TCACATTATCAATTTCTTACACGGATG 58.388 33.333 0.00 0.00 0.00 3.51
4408 4836 8.397906 CACATTATCAATTTCTTACACGGATGT 58.602 33.333 0.00 0.00 43.30 3.06
4417 4845 3.118454 CACGGATGTGGTCGCACC 61.118 66.667 0.00 0.00 42.59 5.01
4418 4846 4.735132 ACGGATGTGGTCGCACCG 62.735 66.667 17.27 17.27 42.58 4.94
4420 4848 4.077184 GGATGTGGTCGCACCGGA 62.077 66.667 9.46 0.00 42.58 5.14
4437 4865 3.320826 ACCGGAATGGAGGTTTCAAAAAG 59.679 43.478 9.46 0.00 42.00 2.27
4455 4883 6.097696 TCAAAAAGGGGGCTGTAAATATAAGC 59.902 38.462 0.00 0.00 36.17 3.09
4468 4896 8.060931 TGTAAATATAAGCCAACAAGCAATCA 57.939 30.769 0.00 0.00 34.23 2.57
4560 4988 7.278135 TCTCATCATCAAGTCCCTTCTATTTG 58.722 38.462 0.00 0.00 0.00 2.32
4601 5029 0.736636 TGGTAGTAGTCATGCCGTCG 59.263 55.000 0.00 0.00 0.00 5.12
4678 5107 2.897969 AGGTCAACTACATTGGTCGTCT 59.102 45.455 0.00 0.00 38.98 4.18
4694 5123 4.056050 GTCGTCTTGAAAGCCTAAAGTCA 58.944 43.478 0.00 0.00 0.00 3.41
4723 5152 1.128200 AGTGTCCAGTAGGTTGCACA 58.872 50.000 0.00 0.00 36.42 4.57
4750 5179 4.380841 AAACCAATAGCAGCATGTCATG 57.619 40.909 8.56 8.56 39.31 3.07
4786 5215 8.610248 TCAACTATCAGATTTTTCCGTTACAA 57.390 30.769 0.00 0.00 0.00 2.41
4820 5249 8.013947 CAGTGTTCATGACTAAGAGTTTGAATG 58.986 37.037 0.00 0.00 35.00 2.67
4861 5290 7.748677 TCAAGATTCATGCCCTCTCAATATAA 58.251 34.615 0.00 0.00 0.00 0.98
4863 5292 9.021807 CAAGATTCATGCCCTCTCAATATAAAT 57.978 33.333 0.00 0.00 0.00 1.40
4864 5293 8.577048 AGATTCATGCCCTCTCAATATAAATG 57.423 34.615 0.00 0.00 0.00 2.32
4866 5295 9.453572 GATTCATGCCCTCTCAATATAAATGTA 57.546 33.333 0.00 0.00 0.00 2.29
4868 5297 8.797350 TCATGCCCTCTCAATATAAATGTATG 57.203 34.615 0.00 0.00 0.00 2.39
4870 5299 9.017509 CATGCCCTCTCAATATAAATGTATGTT 57.982 33.333 0.00 0.00 0.00 2.71
4871 5300 8.621532 TGCCCTCTCAATATAAATGTATGTTC 57.378 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.462240 AGATTAGACTGTCATCCATCCAGA 58.538 41.667 10.88 0.00 0.00 3.86
63 64 6.821388 AGCATTAATTCGGAGATTAGACTGT 58.179 36.000 0.00 0.00 35.04 3.55
65 66 6.268847 AGGAGCATTAATTCGGAGATTAGACT 59.731 38.462 0.00 0.00 35.04 3.24
81 82 5.854010 ACAACTTAGATCGAGGAGCATTA 57.146 39.130 0.00 0.00 0.00 1.90
123 124 4.343814 TCCCAGGACAAGGAAAACAATTTC 59.656 41.667 0.00 0.00 43.46 2.17
127 128 2.243736 AGTCCCAGGACAAGGAAAACAA 59.756 45.455 18.77 0.00 46.76 2.83
141 142 6.487299 AGCCTAAGATAAAAGTAGTCCCAG 57.513 41.667 0.00 0.00 0.00 4.45
157 158 5.904362 ATGAAACTAAAGCCAAGCCTAAG 57.096 39.130 0.00 0.00 0.00 2.18
198 203 9.315525 GAGTTAAAATTCCTGACCTCTACATAC 57.684 37.037 0.00 0.00 0.00 2.39
295 304 1.280710 TCCTCGGTGGTGTAATGCAAT 59.719 47.619 0.00 0.00 37.07 3.56
311 320 8.019656 TCTAACTGGTGGAACTATATTTCCTC 57.980 38.462 19.39 16.12 44.89 3.71
358 367 4.839668 ATCCACATCGACTAGCTAGTTC 57.160 45.455 26.71 17.80 36.50 3.01
371 380 6.995686 TGTACCACCATACAATAATCCACATC 59.004 38.462 0.00 0.00 32.07 3.06
396 405 4.451096 CACGGTTAACTTGCATCTTAGTGT 59.549 41.667 5.42 0.00 0.00 3.55
397 406 4.451096 ACACGGTTAACTTGCATCTTAGTG 59.549 41.667 5.42 3.94 0.00 2.74
403 412 3.551551 GAACACACGGTTAACTTGCATC 58.448 45.455 5.42 0.34 40.63 3.91
416 425 1.320555 CGATAGGCTTTCGAACACACG 59.679 52.381 20.53 0.00 38.88 4.49
417 426 2.334838 ACGATAGGCTTTCGAACACAC 58.665 47.619 29.44 0.00 39.81 3.82
435 444 0.684479 TCCCACATCCTCTGGAGACG 60.684 60.000 0.00 0.00 34.05 4.18
445 454 2.957402 TCATAATGGCTCCCACATCC 57.043 50.000 0.00 0.00 35.80 3.51
461 470 9.521841 AGATGATGATTGCATTCTAAGAATCAT 57.478 29.630 15.61 15.61 44.46 2.45
462 471 8.919777 AGATGATGATTGCATTCTAAGAATCA 57.080 30.769 9.81 9.69 38.75 2.57
524 533 7.164122 AGTTTATGGCTCATCTGTATGTATGG 58.836 38.462 0.00 0.00 34.50 2.74
525 534 8.613060 AAGTTTATGGCTCATCTGTATGTATG 57.387 34.615 0.00 0.00 34.50 2.39
529 538 7.558161 TTGAAGTTTATGGCTCATCTGTATG 57.442 36.000 0.00 0.00 0.00 2.39
535 544 7.867403 TCTTGTTTTTGAAGTTTATGGCTCATC 59.133 33.333 0.00 0.00 0.00 2.92
552 561 8.924511 ACCGATGATATATCCATCTTGTTTTT 57.075 30.769 10.25 0.00 38.53 1.94
602 617 4.278419 AGTGTTTTCCAGACAGTTTATGGC 59.722 41.667 0.00 0.00 37.09 4.40
630 646 2.022764 TGTGGGTGTCATGCTTATCG 57.977 50.000 0.00 0.00 0.00 2.92
637 653 1.471287 CATCTGCTTGTGGGTGTCATG 59.529 52.381 0.00 0.00 0.00 3.07
665 681 5.500234 TGACTGGCTAAAGCATCACTAAAT 58.500 37.500 4.07 0.00 44.36 1.40
803 819 4.074970 GTGAGAGTTGTCCATTCAACCAT 58.925 43.478 6.04 0.00 45.90 3.55
805 821 3.744660 AGTGAGAGTTGTCCATTCAACC 58.255 45.455 6.04 0.00 45.90 3.77
818 834 6.480763 TCTAAAGATGAGACTGAGTGAGAGT 58.519 40.000 0.00 0.00 0.00 3.24
824 840 7.610865 CCTCTTTTCTAAAGATGAGACTGAGT 58.389 38.462 2.62 0.00 0.00 3.41
877 893 2.346284 AAAGCCACCGCCAACCACTA 62.346 55.000 0.00 0.00 34.57 2.74
918 934 1.002134 AAAGCTCATGGACGGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
1061 1116 1.740025 GTAGTAGACGCGGTAGTGGTT 59.260 52.381 12.47 0.00 0.00 3.67
1238 1293 2.104963 GCCGGGAACATTCTATTCTCCT 59.895 50.000 2.18 0.00 0.00 3.69
1471 1526 7.550196 CCCAAAAATTATCAAAATCTGGACTGG 59.450 37.037 0.00 0.00 0.00 4.00
1613 1668 2.093890 CTAATTCTGCCCATGCACACA 58.906 47.619 0.00 0.00 44.23 3.72
1652 1707 3.711704 GAGAGAGAGAGAGGGAGAGAGAA 59.288 52.174 0.00 0.00 0.00 2.87
1656 1711 2.370189 GGAGAGAGAGAGAGAGGGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
1657 1712 2.408565 GGAGAGAGAGAGAGAGGGAGA 58.591 57.143 0.00 0.00 0.00 3.71
1658 1713 1.421646 GGGAGAGAGAGAGAGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
1659 1714 1.518367 GGGAGAGAGAGAGAGAGGGA 58.482 60.000 0.00 0.00 0.00 4.20
1660 1715 0.478507 GGGGAGAGAGAGAGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
1661 1716 0.478507 GGGGGAGAGAGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1662 1717 1.421646 GAGGGGGAGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1663 1718 1.010793 AGAGGGGGAGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
1664 1719 1.522900 AGAGGGGGAGAGAGAGAGAG 58.477 60.000 0.00 0.00 0.00 3.20
1665 1720 1.994399 AAGAGGGGGAGAGAGAGAGA 58.006 55.000 0.00 0.00 0.00 3.10
1666 1721 2.244769 AGAAAGAGGGGGAGAGAGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
1667 1722 2.293246 AGAAAGAGGGGGAGAGAGAGA 58.707 52.381 0.00 0.00 0.00 3.10
1668 1723 2.846665 AGAAAGAGGGGGAGAGAGAG 57.153 55.000 0.00 0.00 0.00 3.20
1669 1724 3.078305 AGAAAGAAAGAGGGGGAGAGAGA 59.922 47.826 0.00 0.00 0.00 3.10
1670 1725 3.449918 AGAAAGAAAGAGGGGGAGAGAG 58.550 50.000 0.00 0.00 0.00 3.20
1671 1726 3.078305 AGAGAAAGAAAGAGGGGGAGAGA 59.922 47.826 0.00 0.00 0.00 3.10
1672 1727 3.449918 AGAGAAAGAAAGAGGGGGAGAG 58.550 50.000 0.00 0.00 0.00 3.20
1673 1728 3.078305 AGAGAGAAAGAAAGAGGGGGAGA 59.922 47.826 0.00 0.00 0.00 3.71
1674 1729 3.449918 AGAGAGAAAGAAAGAGGGGGAG 58.550 50.000 0.00 0.00 0.00 4.30
1675 1730 3.569135 AGAGAGAAAGAAAGAGGGGGA 57.431 47.619 0.00 0.00 0.00 4.81
1676 1731 4.615513 TCTAGAGAGAAAGAAAGAGGGGG 58.384 47.826 0.00 0.00 0.00 5.40
1677 1732 6.136155 AGATCTAGAGAGAAAGAAAGAGGGG 58.864 44.000 0.00 0.00 34.61 4.79
1678 1733 6.833416 TGAGATCTAGAGAGAAAGAAAGAGGG 59.167 42.308 0.00 0.00 34.61 4.30
1679 1734 7.880160 TGAGATCTAGAGAGAAAGAAAGAGG 57.120 40.000 0.00 0.00 34.61 3.69
1684 1753 9.076781 CCACATATGAGATCTAGAGAGAAAGAA 57.923 37.037 10.38 0.00 34.61 2.52
1688 1757 8.637099 CAAACCACATATGAGATCTAGAGAGAA 58.363 37.037 10.38 0.00 34.61 2.87
1719 1788 9.748708 CTGAATTTCTGAGAACAATAAAACCAA 57.251 29.630 0.00 0.00 0.00 3.67
1835 1904 9.662947 CCATGATATATAGAACAGAAGCATGAA 57.337 33.333 0.00 0.00 33.23 2.57
1874 1944 7.386025 TGCAAACATATATGTGAGATCTGCTAC 59.614 37.037 18.94 0.00 41.61 3.58
1877 1947 6.549912 TGCAAACATATATGTGAGATCTGC 57.450 37.500 18.94 18.04 41.61 4.26
1878 1948 8.235226 GGAATGCAAACATATATGTGAGATCTG 58.765 37.037 18.94 10.39 41.61 2.90
1908 1981 8.719560 AAGCTAGGTTTAACTATGACTTAAGC 57.280 34.615 0.12 0.00 0.00 3.09
1947 2020 6.149308 TCAGAAAGGCACTAACATGTAACATG 59.851 38.462 0.00 0.00 38.49 3.21
1958 2031 2.884639 GGTTGCTTCAGAAAGGCACTAA 59.115 45.455 0.00 0.00 38.49 2.24
1959 2032 2.106511 AGGTTGCTTCAGAAAGGCACTA 59.893 45.455 0.00 0.00 38.49 2.74
1962 2035 1.321474 CAGGTTGCTTCAGAAAGGCA 58.679 50.000 0.00 0.00 32.79 4.75
1964 2037 4.616835 GCATAACAGGTTGCTTCAGAAAGG 60.617 45.833 0.00 0.00 35.95 3.11
1970 2051 2.584835 AGGCATAACAGGTTGCTTCA 57.415 45.000 0.00 0.00 38.88 3.02
2056 2137 7.883217 TGAACAAGAGATCGAGTACTACTTTT 58.117 34.615 0.00 0.00 0.00 2.27
2084 2165 8.387190 AGTTTATTAATTAACCTGGGCGATAC 57.613 34.615 12.48 0.00 0.00 2.24
2085 2166 8.983702 AAGTTTATTAATTAACCTGGGCGATA 57.016 30.769 12.48 0.00 0.00 2.92
2110 2191 0.690192 TGCAGGGAATTTGGAGACGA 59.310 50.000 0.00 0.00 0.00 4.20
2112 2193 0.813821 GCTGCAGGGAATTTGGAGAC 59.186 55.000 17.12 0.00 36.24 3.36
2113 2194 0.405198 TGCTGCAGGGAATTTGGAGA 59.595 50.000 17.12 0.00 36.24 3.71
2116 2197 1.406341 CCATTGCTGCAGGGAATTTGG 60.406 52.381 17.12 5.86 33.68 3.28
2123 2204 1.735376 GCATCTCCATTGCTGCAGGG 61.735 60.000 17.12 14.21 37.14 4.45
2333 2415 3.572682 TCCTTAGTGACTCGTTCATGTGT 59.427 43.478 0.00 0.00 36.32 3.72
2469 2558 1.072965 GGGCCAGGAACAGATCATAGG 59.927 57.143 4.39 0.00 0.00 2.57
2615 2707 3.388308 GCACCAACATGCATGTGTAAAA 58.612 40.909 31.98 0.00 45.39 1.52
2698 2790 2.218603 CTACCAAAAAGACGTGTGCCT 58.781 47.619 0.00 0.00 0.00 4.75
2757 2850 6.095440 GCAAAGTGATAATTTCCTCTGCCTTA 59.905 38.462 0.00 0.00 0.00 2.69
2766 2859 6.724694 TTGCAATGCAAAGTGATAATTTCC 57.275 33.333 19.21 0.00 45.96 3.13
2805 2898 0.109153 CTGGATGGGATCGATGGCAA 59.891 55.000 0.54 0.00 0.00 4.52
2821 2914 3.731652 TGAAAGTGAAAATGCACCTGG 57.268 42.857 0.00 0.00 39.59 4.45
2952 3045 2.224793 GGTTTGGTAGGCTTTCTCCAGT 60.225 50.000 0.00 0.00 0.00 4.00
3051 3144 2.123854 ATAGAGCCGCCGAGGTCA 60.124 61.111 7.36 0.00 43.70 4.02
3066 3159 2.550277 TGAGGTCCTGGAAGCTCATA 57.450 50.000 17.95 3.84 45.98 2.15
3087 3180 2.037136 CGACGACCCTCCGTACAGT 61.037 63.158 0.00 0.00 43.49 3.55
3246 3339 2.203112 GCCTGCTCATCATCGCCA 60.203 61.111 0.00 0.00 0.00 5.69
3285 3378 1.591059 CGCCATCTGGAGAAGCTCG 60.591 63.158 0.00 0.00 37.14 5.03
3498 3591 6.144724 TGTTTCCAAAGAAGAACAAAAACACG 59.855 34.615 0.00 0.00 32.27 4.49
3610 3704 0.103208 CTTAGCTACACCTCAGCCCG 59.897 60.000 0.00 0.00 39.99 6.13
3715 3809 7.091443 CCTTAAACCAACGCCAATATGTTAAA 58.909 34.615 0.00 0.00 0.00 1.52
3747 3842 4.620982 GCTTTCACAGCTACACCAAAATT 58.379 39.130 0.00 0.00 46.27 1.82
3922 4030 9.030452 ACATGGCCTTTAATCACAACTTAATTA 57.970 29.630 3.32 0.00 0.00 1.40
4145 4557 9.553064 GACTAATTGTGACTCATAATTCAGGAT 57.447 33.333 14.94 1.50 36.73 3.24
4346 4758 8.089625 TCCATCTGTTTCCTTTCATAGTATGA 57.910 34.615 8.84 8.84 37.55 2.15
4355 4767 5.163713 GCATACACTCCATCTGTTTCCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
4390 4803 4.435518 CGACCACATCCGTGTAAGAAATTG 60.436 45.833 0.00 0.00 41.93 2.32
4406 4834 2.358125 CATTCCGGTGCGACCACA 60.358 61.111 0.00 0.00 43.88 4.17
4407 4835 3.124921 CCATTCCGGTGCGACCAC 61.125 66.667 0.00 0.00 38.47 4.16
4408 4836 3.309436 CTCCATTCCGGTGCGACCA 62.309 63.158 0.00 0.00 38.47 4.02
4409 4837 2.511600 CTCCATTCCGGTGCGACC 60.512 66.667 0.00 0.00 35.57 4.79
4410 4838 2.511600 CCTCCATTCCGGTGCGAC 60.512 66.667 0.00 0.00 35.57 5.19
4411 4839 2.119484 AAACCTCCATTCCGGTGCGA 62.119 55.000 0.00 0.00 35.57 5.10
4412 4840 1.644786 GAAACCTCCATTCCGGTGCG 61.645 60.000 0.00 0.00 35.57 5.34
4413 4841 0.608035 TGAAACCTCCATTCCGGTGC 60.608 55.000 0.00 0.00 35.57 5.01
4414 4842 1.904287 TTGAAACCTCCATTCCGGTG 58.096 50.000 0.00 0.00 35.57 4.94
4415 4843 2.668144 TTTGAAACCTCCATTCCGGT 57.332 45.000 0.00 0.00 35.57 5.28
4416 4844 3.306019 CCTTTTTGAAACCTCCATTCCGG 60.306 47.826 0.00 0.00 0.00 5.14
4417 4845 3.306019 CCCTTTTTGAAACCTCCATTCCG 60.306 47.826 0.00 0.00 0.00 4.30
4418 4846 3.007940 CCCCTTTTTGAAACCTCCATTCC 59.992 47.826 0.00 0.00 0.00 3.01
4419 4847 3.007940 CCCCCTTTTTGAAACCTCCATTC 59.992 47.826 0.00 0.00 0.00 2.67
4420 4848 2.978978 CCCCCTTTTTGAAACCTCCATT 59.021 45.455 0.00 0.00 0.00 3.16
4455 4883 3.181483 GGAAGGCTATGATTGCTTGTTGG 60.181 47.826 0.00 0.00 0.00 3.77
4579 5007 3.190744 CGACGGCATGACTACTACCATAT 59.809 47.826 0.00 0.00 0.00 1.78
4584 5012 0.737219 ACCGACGGCATGACTACTAC 59.263 55.000 15.39 0.00 0.00 2.73
4586 5014 0.606604 AAACCGACGGCATGACTACT 59.393 50.000 15.39 0.00 0.00 2.57
4587 5015 2.282701 TAAACCGACGGCATGACTAC 57.717 50.000 15.39 0.00 0.00 2.73
4702 5131 2.143925 GTGCAACCTACTGGACACTTC 58.856 52.381 0.00 0.00 37.57 3.01
4709 5138 5.335661 GGTTTAGAAATGTGCAACCTACTGG 60.336 44.000 0.00 0.00 35.05 4.00
4711 5140 5.381757 TGGTTTAGAAATGTGCAACCTACT 58.618 37.500 0.00 0.00 38.20 2.57
4723 5152 6.377996 TGACATGCTGCTATTGGTTTAGAAAT 59.622 34.615 0.00 0.00 0.00 2.17
4786 5215 9.823647 CTCTTAGTCATGAACACTGGTTATATT 57.176 33.333 0.00 0.00 37.36 1.28
4793 5222 5.991606 TCAAACTCTTAGTCATGAACACTGG 59.008 40.000 0.00 0.00 0.00 4.00
4820 5249 6.919662 TGAATCTTGATGCAAAGTTCAAACTC 59.080 34.615 0.00 0.00 38.57 3.01


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

AutoCloner maintained by Alex Coulton.