Multiple sequence alignment - TraesCS5D01G535500

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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 TraesCS5D01G535500 chr5D 100.000 3054 0 0 1 3054 549332231 549329178 0.000000e+00 5640.0
1 TraesCS5D01G535500 chr5D 84.451 328 48 3 1332 1657 544799360 544799686 1.370000e-83 320.0
2 TraesCS5D01G535500 chr5B 94.114 1648 55 18 39 1656 700996271 700997906 0.000000e+00 2468.0
3 TraesCS5D01G535500 chr5B 81.993 883 83 33 2213 3051 700998399 700999249 0.000000e+00 680.0
4 TraesCS5D01G535500 chr5B 90.300 433 24 13 1743 2169 700997904 700998324 4.450000e-153 551.0
5 TraesCS5D01G535500 chr5B 82.927 328 52 4 1332 1657 687212999 687213324 2.980000e-75 292.0
6 TraesCS5D01G535500 chr4A 92.021 1341 73 17 1743 3054 621009427 621008092 0.000000e+00 1853.0
7 TraesCS5D01G535500 chr4A 93.056 1152 62 10 1 1145 621011412 621010272 0.000000e+00 1668.0
8 TraesCS5D01G535500 chr4A 97.527 364 8 1 1294 1656 621009788 621009425 3.340000e-174 621.0
9 TraesCS5D01G535500 chr4A 84.713 314 44 4 1339 1650 26413808 26413497 8.220000e-81 311.0
10 TraesCS5D01G535500 chr4B 84.466 309 48 0 1336 1644 547205034 547205342 3.830000e-79 305.0
11 TraesCS5D01G535500 chr1B 84.076 314 42 8 1334 1643 264763400 264763709 2.300000e-76 296.0
12 TraesCS5D01G535500 chr4D 83.871 310 48 2 1336 1644 441132113 441132421 8.280000e-76 294.0
13 TraesCS5D01G535500 chr4D 82.555 321 46 9 1335 1650 442215099 442214784 1.080000e-69 274.0
14 TraesCS5D01G535500 chr2B 81.065 169 28 2 2329 2497 58682773 58682937 6.870000e-27 132.0
15 TraesCS5D01G535500 chr2B 85.417 96 8 6 2409 2501 482728213 482728305 9.010000e-16 95.3
16 TraesCS5D01G535500 chr6A 86.598 97 10 3 2407 2501 600949219 600949124 1.500000e-18 104.0
17 TraesCS5D01G535500 chr6D 82.418 91 13 2 2407 2497 363319369 363319456 3.270000e-10 76.8
18 TraesCS5D01G535500 chr7A 100.000 28 0 0 2468 2495 428826347 428826320 6.000000e-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 TraesCS5D01G535500 chr5D 549329178 549332231 3053 True 5640.000000 5640 100.000000 1 3054 1 chr5D.!!$R1 3053
1 TraesCS5D01G535500 chr5B 700996271 700999249 2978 False 1233.000000 2468 88.802333 39 3051 3 chr5B.!!$F2 3012
2 TraesCS5D01G535500 chr4A 621008092 621011412 3320 True 1380.666667 1853 94.201333 1 3054 3 chr4A.!!$R2 3053

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
981 995 0.039074 ACTACAGCGCTGTGTCTGTC 60.039 55.0 44.69 0.0 44.63 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2659 0.175302 TTGTGTGCTTGCCTGGTTTG 59.825 50.0 0.0 0.0 0.0 2.93 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
107 108 2.747989 GCCTCCTGTTAGTTTAGCCAAC 59.252 50.000 0.00 0.00 35.32 3.77
114 115 8.700439 TCCTGTTAGTTTAGCCAACTTAAATT 57.300 30.769 4.30 0.00 43.89 1.82
237 240 0.594796 GTCAAGCGGTGGTGCAAAAG 60.595 55.000 0.00 0.00 37.31 2.27
290 293 4.274214 CGTCGGTGAGGTATAAGTGATACA 59.726 45.833 0.00 0.00 42.11 2.29
293 296 5.475909 TCGGTGAGGTATAAGTGATACATCC 59.524 44.000 9.36 2.23 46.66 3.51
440 447 3.495377 CGACAAAAGTCGGTGGACAAATA 59.505 43.478 9.94 0.00 45.92 1.40
590 597 2.833794 TGGTCAGACTCTTTGTTTCCG 58.166 47.619 0.00 0.00 0.00 4.30
681 688 1.283793 GGCACATGCACACTGACAC 59.716 57.895 6.15 0.00 44.36 3.67
709 716 4.201656 GGAATTTGTCGACGCCTAGTTAAC 60.202 45.833 11.62 0.00 0.00 2.01
716 723 4.009675 TCGACGCCTAGTTAACCTTCTTA 58.990 43.478 0.88 0.00 0.00 2.10
802 809 5.127845 TGTGCCAAAAGTCAAATAAGGAACA 59.872 36.000 0.00 0.00 30.94 3.18
804 811 6.019075 GTGCCAAAAGTCAAATAAGGAACAAC 60.019 38.462 0.00 0.00 0.00 3.32
835 844 3.133542 GCTAAGTTAACCCGAGTACCCAT 59.866 47.826 0.88 0.00 0.00 4.00
846 855 3.194968 CCGAGTACCCATCTACAACTGTT 59.805 47.826 0.00 0.00 0.00 3.16
848 857 5.105635 CCGAGTACCCATCTACAACTGTTAA 60.106 44.000 0.00 0.00 0.00 2.01
849 858 5.803967 CGAGTACCCATCTACAACTGTTAAC 59.196 44.000 0.00 0.00 0.00 2.01
850 859 6.570957 CGAGTACCCATCTACAACTGTTAACA 60.571 42.308 8.28 8.28 0.00 2.41
935 944 2.926200 CAGTACACAGAGCACAGCATAC 59.074 50.000 0.00 0.00 0.00 2.39
979 993 1.200252 AGTACTACAGCGCTGTGTCTG 59.800 52.381 44.69 32.50 44.63 3.51
980 994 1.068472 GTACTACAGCGCTGTGTCTGT 60.068 52.381 44.69 35.26 44.63 3.41
981 995 0.039074 ACTACAGCGCTGTGTCTGTC 60.039 55.000 44.69 0.00 44.63 3.51
1071 1085 2.088104 TAGCTTCTCATGGGGTCGAT 57.912 50.000 0.00 0.00 0.00 3.59
1182 1204 8.146053 TCTTTACTTTCCTGTATCATTCTCCA 57.854 34.615 0.00 0.00 0.00 3.86
1199 1221 0.538584 CCAGTGGAGAGTGCATAGCA 59.461 55.000 1.68 0.00 35.60 3.49
1218 1244 7.117523 GCATAGCATCTAAATCTCTAGTTGTGG 59.882 40.741 0.00 0.00 0.00 4.17
1221 1247 5.988561 GCATCTAAATCTCTAGTTGTGGAGG 59.011 44.000 0.00 0.00 32.16 4.30
1281 1619 7.921214 CGTTTGGTGTGATATACTCTACTCATT 59.079 37.037 0.00 0.00 0.00 2.57
1319 1675 9.181061 TGATGTTGATCTGATGATGTTTGTATT 57.819 29.630 0.00 0.00 32.19 1.89
1325 1681 8.562052 TGATCTGATGATGTTTGTATTGTATGC 58.438 33.333 0.00 0.00 32.19 3.14
1655 2022 2.707849 CCCCGTCGTGTACAGGAGG 61.708 68.421 24.28 24.28 0.00 4.30
1656 2023 1.975407 CCCGTCGTGTACAGGAGGT 60.975 63.158 27.12 0.00 31.50 3.85
1657 2024 1.211969 CCGTCGTGTACAGGAGGTG 59.788 63.158 27.12 18.51 31.50 4.00
1658 2025 1.239296 CCGTCGTGTACAGGAGGTGA 61.239 60.000 27.12 4.11 31.50 4.02
1659 2026 0.809385 CGTCGTGTACAGGAGGTGAT 59.191 55.000 23.38 0.00 0.00 3.06
1660 2027 1.201647 CGTCGTGTACAGGAGGTGATT 59.798 52.381 23.38 0.00 0.00 2.57
1661 2028 2.421073 CGTCGTGTACAGGAGGTGATTA 59.579 50.000 23.38 0.00 0.00 1.75
1662 2029 3.730061 CGTCGTGTACAGGAGGTGATTAC 60.730 52.174 23.38 9.11 0.00 1.89
1676 2043 2.415168 GTGATTACCACATCCACACACG 59.585 50.000 0.00 0.00 45.03 4.49
1677 2044 2.300437 TGATTACCACATCCACACACGA 59.700 45.455 0.00 0.00 0.00 4.35
1678 2045 2.448926 TTACCACATCCACACACGAG 57.551 50.000 0.00 0.00 0.00 4.18
1679 2046 1.623163 TACCACATCCACACACGAGA 58.377 50.000 0.00 0.00 0.00 4.04
1680 2047 0.318441 ACCACATCCACACACGAGAG 59.682 55.000 0.00 0.00 0.00 3.20
1682 2049 1.270305 CCACATCCACACACGAGAGTT 60.270 52.381 0.00 0.00 46.40 3.01
1683 2050 1.794701 CACATCCACACACGAGAGTTG 59.205 52.381 0.00 0.00 46.40 3.16
1684 2051 1.686587 ACATCCACACACGAGAGTTGA 59.313 47.619 0.00 0.00 46.40 3.18
1685 2052 2.300152 ACATCCACACACGAGAGTTGAT 59.700 45.455 0.00 0.00 46.40 2.57
1686 2053 3.509967 ACATCCACACACGAGAGTTGATA 59.490 43.478 0.00 0.00 46.40 2.15
1687 2054 3.850122 TCCACACACGAGAGTTGATAG 57.150 47.619 0.00 0.00 46.40 2.08
1688 2055 3.154710 TCCACACACGAGAGTTGATAGT 58.845 45.455 0.00 0.00 46.40 2.12
1689 2056 3.572682 TCCACACACGAGAGTTGATAGTT 59.427 43.478 0.00 0.00 46.40 2.24
1690 2057 3.675225 CCACACACGAGAGTTGATAGTTG 59.325 47.826 0.00 0.00 46.40 3.16
1691 2058 4.546570 CACACACGAGAGTTGATAGTTGA 58.453 43.478 0.00 0.00 46.40 3.18
1692 2059 5.164233 CACACACGAGAGTTGATAGTTGAT 58.836 41.667 0.00 0.00 46.40 2.57
1693 2060 6.322491 CACACACGAGAGTTGATAGTTGATA 58.678 40.000 0.00 0.00 46.40 2.15
1694 2061 6.975197 CACACACGAGAGTTGATAGTTGATAT 59.025 38.462 0.00 0.00 46.40 1.63
1695 2062 7.166638 CACACACGAGAGTTGATAGTTGATATC 59.833 40.741 0.00 0.00 46.40 1.63
1696 2063 7.067615 ACACACGAGAGTTGATAGTTGATATCT 59.932 37.037 3.98 0.00 46.40 1.98
1697 2064 8.560374 CACACGAGAGTTGATAGTTGATATCTA 58.440 37.037 3.98 0.00 46.40 1.98
1698 2065 8.561212 ACACGAGAGTTGATAGTTGATATCTAC 58.439 37.037 9.01 9.01 46.40 2.59
1699 2066 7.742525 CACGAGAGTTGATAGTTGATATCTACG 59.257 40.741 10.95 0.00 45.63 3.51
1700 2067 6.739100 CGAGAGTTGATAGTTGATATCTACGC 59.261 42.308 10.95 6.36 45.63 4.42
1701 2068 7.511959 AGAGTTGATAGTTGATATCTACGCA 57.488 36.000 10.95 8.46 45.63 5.24
1702 2069 7.589395 AGAGTTGATAGTTGATATCTACGCAG 58.411 38.462 10.95 0.00 45.63 5.18
1703 2070 7.445707 AGAGTTGATAGTTGATATCTACGCAGA 59.554 37.037 10.95 0.00 45.63 4.26
1704 2071 8.116651 AGTTGATAGTTGATATCTACGCAGAT 57.883 34.615 10.95 3.15 45.63 2.90
1705 2072 8.240682 AGTTGATAGTTGATATCTACGCAGATC 58.759 37.037 0.17 12.04 45.63 2.75
1706 2073 7.929941 TGATAGTTGATATCTACGCAGATCT 57.070 36.000 0.17 0.00 40.81 2.75
1707 2074 8.341892 TGATAGTTGATATCTACGCAGATCTT 57.658 34.615 0.17 0.00 40.81 2.40
1708 2075 8.797438 TGATAGTTGATATCTACGCAGATCTTT 58.203 33.333 0.17 0.00 40.81 2.52
1709 2076 9.632807 GATAGTTGATATCTACGCAGATCTTTT 57.367 33.333 0.17 0.00 40.81 2.27
1710 2077 7.706281 AGTTGATATCTACGCAGATCTTTTG 57.294 36.000 0.17 0.00 40.81 2.44
1711 2078 7.268586 AGTTGATATCTACGCAGATCTTTTGT 58.731 34.615 0.17 0.00 40.81 2.83
1712 2079 8.414003 AGTTGATATCTACGCAGATCTTTTGTA 58.586 33.333 0.17 0.00 40.81 2.41
1713 2080 9.197694 GTTGATATCTACGCAGATCTTTTGTAT 57.802 33.333 0.17 0.00 40.81 2.29
1714 2081 8.748380 TGATATCTACGCAGATCTTTTGTATG 57.252 34.615 0.17 0.00 40.81 2.39
1715 2082 8.576442 TGATATCTACGCAGATCTTTTGTATGA 58.424 33.333 0.17 0.00 40.81 2.15
1716 2083 9.411801 GATATCTACGCAGATCTTTTGTATGAA 57.588 33.333 0.17 0.00 40.81 2.57
1717 2084 7.706281 ATCTACGCAGATCTTTTGTATGAAG 57.294 36.000 0.00 0.00 36.80 3.02
1718 2085 4.606457 ACGCAGATCTTTTGTATGAAGC 57.394 40.909 0.00 0.00 0.00 3.86
1719 2086 3.062639 ACGCAGATCTTTTGTATGAAGCG 59.937 43.478 13.21 13.21 45.96 4.68
1720 2087 3.306973 CGCAGATCTTTTGTATGAAGCGA 59.693 43.478 10.22 0.00 43.59 4.93
1721 2088 4.025396 CGCAGATCTTTTGTATGAAGCGAT 60.025 41.667 10.22 0.00 43.59 4.58
1722 2089 5.203370 GCAGATCTTTTGTATGAAGCGATG 58.797 41.667 0.00 0.00 0.00 3.84
1723 2090 5.203370 CAGATCTTTTGTATGAAGCGATGC 58.797 41.667 0.00 0.00 0.00 3.91
1724 2091 5.007430 CAGATCTTTTGTATGAAGCGATGCT 59.993 40.000 0.00 0.00 42.56 3.79
1725 2092 6.201615 CAGATCTTTTGTATGAAGCGATGCTA 59.798 38.462 0.00 0.00 38.25 3.49
1726 2093 5.718649 TCTTTTGTATGAAGCGATGCTAC 57.281 39.130 0.00 0.00 38.25 3.58
1727 2094 5.419542 TCTTTTGTATGAAGCGATGCTACT 58.580 37.500 0.00 0.00 38.25 2.57
1728 2095 5.874810 TCTTTTGTATGAAGCGATGCTACTT 59.125 36.000 0.00 0.00 38.25 2.24
1729 2096 5.718649 TTTGTATGAAGCGATGCTACTTC 57.281 39.130 0.00 0.00 38.25 3.01
1733 2100 3.319137 TGAAGCGATGCTACTTCACTT 57.681 42.857 1.49 0.00 45.48 3.16
1734 2101 2.995939 TGAAGCGATGCTACTTCACTTG 59.004 45.455 1.49 0.00 45.48 3.16
1735 2102 2.751166 AGCGATGCTACTTCACTTGT 57.249 45.000 0.00 0.00 36.99 3.16
1736 2103 2.341257 AGCGATGCTACTTCACTTGTG 58.659 47.619 0.00 0.00 36.99 3.33
1737 2104 1.201965 GCGATGCTACTTCACTTGTGC 60.202 52.381 0.00 0.00 0.00 4.57
1738 2105 1.394917 CGATGCTACTTCACTTGTGCC 59.605 52.381 0.00 0.00 0.00 5.01
1739 2106 2.704572 GATGCTACTTCACTTGTGCCT 58.295 47.619 0.00 0.00 0.00 4.75
1740 2107 1.882912 TGCTACTTCACTTGTGCCTG 58.117 50.000 0.00 0.00 0.00 4.85
1741 2108 0.519077 GCTACTTCACTTGTGCCTGC 59.481 55.000 0.00 0.00 0.00 4.85
1742 2109 1.882912 CTACTTCACTTGTGCCTGCA 58.117 50.000 0.00 0.00 0.00 4.41
1743 2110 1.802960 CTACTTCACTTGTGCCTGCAG 59.197 52.381 6.78 6.78 0.00 4.41
1747 2114 2.203394 ACTTGTGCCTGCAGGGTG 60.203 61.111 33.46 9.60 37.43 4.61
1750 2117 4.624364 TGTGCCTGCAGGGTGTCG 62.624 66.667 33.46 8.00 37.43 4.35
1816 2183 1.669115 CTTCGAGCTGGTGGTGGTG 60.669 63.158 0.00 0.00 0.00 4.17
2041 2408 0.324943 CCACCTACACTTCCTGGGTG 59.675 60.000 0.00 0.00 44.77 4.61
2061 2428 4.874966 GGTGAACTTCTACTAGCGTCTAGA 59.125 45.833 17.20 0.00 0.00 2.43
2071 2438 4.720046 ACTAGCGTCTAGAGGATCATCAA 58.280 43.478 16.47 0.00 37.82 2.57
2072 2439 5.133941 ACTAGCGTCTAGAGGATCATCAAA 58.866 41.667 16.47 0.00 37.82 2.69
2073 2440 4.314740 AGCGTCTAGAGGATCATCAAAC 57.685 45.455 16.47 3.71 37.82 2.93
2074 2441 3.068873 AGCGTCTAGAGGATCATCAAACC 59.931 47.826 16.47 0.14 37.82 3.27
2076 2443 4.615949 CGTCTAGAGGATCATCAAACCAG 58.384 47.826 10.44 0.00 37.82 4.00
2077 2444 4.098654 CGTCTAGAGGATCATCAAACCAGT 59.901 45.833 10.44 0.00 37.82 4.00
2078 2445 5.596845 GTCTAGAGGATCATCAAACCAGTC 58.403 45.833 10.44 0.00 37.82 3.51
2079 2446 3.533606 AGAGGATCATCAAACCAGTCG 57.466 47.619 10.44 0.00 37.82 4.18
2189 2567 3.898509 GTGTTTGGCAGCCGCACA 61.899 61.111 21.67 16.98 41.24 4.57
2190 2568 2.911509 TGTTTGGCAGCCGCACAT 60.912 55.556 7.03 0.00 41.24 3.21
2191 2569 2.339712 GTTTGGCAGCCGCACATT 59.660 55.556 7.03 0.00 41.24 2.71
2198 2576 0.098728 GCAGCCGCACATTATTCGTT 59.901 50.000 0.00 0.00 38.36 3.85
2200 2578 1.396648 CAGCCGCACATTATTCGTTCA 59.603 47.619 0.00 0.00 0.00 3.18
2208 2586 6.194508 CCGCACATTATTCGTTCATGTTTTAG 59.805 38.462 0.00 0.00 0.00 1.85
2210 2588 7.162546 CGCACATTATTCGTTCATGTTTTAGAG 59.837 37.037 0.00 0.00 0.00 2.43
2254 2659 6.743575 ACACATAATAACCTGAAGCTTCAC 57.256 37.500 25.16 1.07 32.90 3.18
2325 2739 3.861113 TGTACGAAATGAAGACGGCATAC 59.139 43.478 0.00 0.00 0.00 2.39
2452 2872 9.651913 TCCAAATTAAGTTTCCTTTGCATATTC 57.348 29.630 0.00 0.00 31.89 1.75
2513 2960 9.019764 CATTTTGAATCGTTAAGTTTCAACTGT 57.980 29.630 4.40 0.00 43.94 3.55
2532 2979 6.072112 ACTGTTGAAACATGGTATGACAAC 57.928 37.500 12.72 12.72 38.41 3.32
2537 2984 5.937187 TGAAACATGGTATGACAACAATCG 58.063 37.500 0.00 0.00 0.00 3.34
2546 2993 6.261158 TGGTATGACAACAATCGAAGTTTCAA 59.739 34.615 15.53 3.99 0.00 2.69
2597 3044 4.330944 AATGCGGTATCCATCGAGTTTA 57.669 40.909 0.00 0.00 0.00 2.01
2735 3189 5.056894 TCAAACCGAGCTAAACTAGTCTC 57.943 43.478 0.00 0.00 0.00 3.36
2736 3190 4.521639 TCAAACCGAGCTAAACTAGTCTCA 59.478 41.667 0.00 0.00 32.28 3.27
2771 3225 0.321298 GCAACTCGAGGCAACCCTAA 60.321 55.000 18.41 0.00 43.12 2.69
2797 3252 0.978146 CCCACCTCCCTCGATGAACT 60.978 60.000 0.00 0.00 0.00 3.01
2846 3301 1.343176 GGCCACTCCTACCCTAGAAGT 60.343 57.143 0.00 0.00 0.00 3.01
2872 3327 3.305709 CGGAGCTTGAGGTGAACAA 57.694 52.632 0.00 0.00 0.00 2.83
2895 3350 2.045708 GCCATGGCGGTCAACATCA 61.046 57.895 23.48 0.00 36.97 3.07
2921 3376 0.859232 GTGCGACTTGCTTTTCGAGA 59.141 50.000 5.73 0.00 46.63 4.04
3032 3487 1.613925 GATGCGTGGGTGCTAGATCTA 59.386 52.381 1.69 1.69 35.36 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.327924 TAGTGTACCTTCCGGACGGA 59.672 55.000 32.17 13.76 43.52 4.69
31 32 2.865343 ATGCTACGCACTAGTGTACC 57.135 50.000 23.44 6.81 43.04 3.34
107 108 9.979270 GTGTCATGTTCTGATCTGTAATTTAAG 57.021 33.333 0.00 0.00 35.97 1.85
114 115 5.127194 GGGTAGTGTCATGTTCTGATCTGTA 59.873 44.000 0.00 0.00 35.97 2.74
118 119 4.160439 TCAGGGTAGTGTCATGTTCTGATC 59.840 45.833 0.00 0.00 35.97 2.92
130 131 3.840991 TCTACTGTTGTCAGGGTAGTGT 58.159 45.455 0.00 0.00 45.14 3.55
171 174 0.250640 CACACAAGGCAAGAGCTCCT 60.251 55.000 10.93 0.00 41.70 3.69
290 293 2.884012 TGTTTTTGCACATCTCACGGAT 59.116 40.909 0.00 0.00 34.51 4.18
293 296 3.631144 ACATGTTTTTGCACATCTCACG 58.369 40.909 0.00 0.00 35.03 4.35
422 429 3.818773 CCTGTATTTGTCCACCGACTTTT 59.181 43.478 0.00 0.00 39.94 2.27
440 447 2.187958 TCCGAATGGATCTCAACCTGT 58.812 47.619 0.00 0.00 40.17 4.00
590 597 4.525912 AATTCAACCAGAACAAGATGGC 57.474 40.909 0.00 0.00 40.45 4.40
681 688 0.179215 GCGTCGACAAATTCCTGCAG 60.179 55.000 17.16 6.78 0.00 4.41
709 716 5.296283 CCATGTTCTTGATGCTCTAAGAAGG 59.704 44.000 9.16 5.40 41.90 3.46
716 723 3.708403 TCACCATGTTCTTGATGCTCT 57.292 42.857 0.00 0.00 0.00 4.09
802 809 1.259840 TAACTTAGCCGCCCTCCGTT 61.260 55.000 0.00 0.00 34.38 4.44
804 811 0.808847 GTTAACTTAGCCGCCCTCCG 60.809 60.000 0.00 0.00 0.00 4.63
846 855 7.324935 TGCATATCCTCTAACGAAAACTGTTA 58.675 34.615 0.00 0.00 0.00 2.41
848 857 5.730550 TGCATATCCTCTAACGAAAACTGT 58.269 37.500 0.00 0.00 0.00 3.55
849 858 6.653183 CATGCATATCCTCTAACGAAAACTG 58.347 40.000 0.00 0.00 0.00 3.16
850 859 5.237344 GCATGCATATCCTCTAACGAAAACT 59.763 40.000 14.21 0.00 0.00 2.66
851 860 5.237344 AGCATGCATATCCTCTAACGAAAAC 59.763 40.000 21.98 0.00 0.00 2.43
852 861 5.368145 AGCATGCATATCCTCTAACGAAAA 58.632 37.500 21.98 0.00 0.00 2.29
853 862 4.960938 AGCATGCATATCCTCTAACGAAA 58.039 39.130 21.98 0.00 0.00 3.46
854 863 4.039124 TGAGCATGCATATCCTCTAACGAA 59.961 41.667 21.98 0.00 0.00 3.85
855 864 3.573967 TGAGCATGCATATCCTCTAACGA 59.426 43.478 21.98 0.00 0.00 3.85
856 865 3.917988 TGAGCATGCATATCCTCTAACG 58.082 45.455 21.98 0.00 0.00 3.18
935 944 1.202359 GCCGAGCAAGTCTTCTAGGAG 60.202 57.143 12.26 0.00 0.00 3.69
979 993 5.327091 CATTGGATTGTTGAAGATGACGAC 58.673 41.667 0.00 0.00 0.00 4.34
980 994 4.395854 CCATTGGATTGTTGAAGATGACGA 59.604 41.667 0.00 0.00 0.00 4.20
981 995 4.439153 CCCATTGGATTGTTGAAGATGACG 60.439 45.833 3.62 0.00 0.00 4.35
1023 1037 0.243907 GCACACCGAGAAGCACTAGA 59.756 55.000 0.00 0.00 0.00 2.43
1182 1204 2.396608 AGATGCTATGCACTCTCCACT 58.603 47.619 0.00 0.00 43.04 4.00
1197 1219 5.988561 CCTCCACAACTAGAGATTTAGATGC 59.011 44.000 0.00 0.00 31.43 3.91
1199 1221 6.098982 CACCCTCCACAACTAGAGATTTAGAT 59.901 42.308 0.00 0.00 31.43 1.98
1218 1244 4.904895 ACTCTACCCTTTAAACACCCTC 57.095 45.455 0.00 0.00 0.00 4.30
1221 1247 8.319881 AGAAATCTACTCTACCCTTTAAACACC 58.680 37.037 0.00 0.00 0.00 4.16
1252 1585 7.701445 AGTAGAGTATATCACACCAAACGTAC 58.299 38.462 0.00 0.00 0.00 3.67
1281 1619 5.936372 CAGATCAACATCACTTCTCCTTTGA 59.064 40.000 0.00 0.00 0.00 2.69
1325 1681 2.601398 CGCGCCTCCTGCATACATG 61.601 63.158 0.00 0.00 41.33 3.21
1655 2022 2.415168 CGTGTGTGGATGTGGTAATCAC 59.585 50.000 0.00 0.00 46.23 3.06
1656 2023 2.300437 TCGTGTGTGGATGTGGTAATCA 59.700 45.455 0.00 0.00 0.00 2.57
1657 2024 2.930040 CTCGTGTGTGGATGTGGTAATC 59.070 50.000 0.00 0.00 0.00 1.75
1658 2025 2.565391 TCTCGTGTGTGGATGTGGTAAT 59.435 45.455 0.00 0.00 0.00 1.89
1659 2026 1.964933 TCTCGTGTGTGGATGTGGTAA 59.035 47.619 0.00 0.00 0.00 2.85
1660 2027 1.544246 CTCTCGTGTGTGGATGTGGTA 59.456 52.381 0.00 0.00 0.00 3.25
1661 2028 0.318441 CTCTCGTGTGTGGATGTGGT 59.682 55.000 0.00 0.00 0.00 4.16
1662 2029 0.318441 ACTCTCGTGTGTGGATGTGG 59.682 55.000 0.00 0.00 0.00 4.17
1663 2030 1.794701 CAACTCTCGTGTGTGGATGTG 59.205 52.381 0.00 0.00 0.00 3.21
1664 2031 1.686587 TCAACTCTCGTGTGTGGATGT 59.313 47.619 0.00 0.00 0.00 3.06
1665 2032 2.438868 TCAACTCTCGTGTGTGGATG 57.561 50.000 0.00 0.00 0.00 3.51
1666 2033 3.764434 ACTATCAACTCTCGTGTGTGGAT 59.236 43.478 12.64 12.64 35.34 3.41
1667 2034 3.154710 ACTATCAACTCTCGTGTGTGGA 58.845 45.455 0.00 0.00 0.00 4.02
1668 2035 3.577649 ACTATCAACTCTCGTGTGTGG 57.422 47.619 0.00 0.00 0.00 4.17
1669 2036 4.546570 TCAACTATCAACTCTCGTGTGTG 58.453 43.478 0.00 0.00 0.00 3.82
1670 2037 4.848562 TCAACTATCAACTCTCGTGTGT 57.151 40.909 0.00 0.00 0.00 3.72
1671 2038 7.421599 AGATATCAACTATCAACTCTCGTGTG 58.578 38.462 5.32 0.00 39.03 3.82
1672 2039 7.575414 AGATATCAACTATCAACTCTCGTGT 57.425 36.000 5.32 0.00 39.03 4.49
1673 2040 7.742525 CGTAGATATCAACTATCAACTCTCGTG 59.257 40.741 5.32 0.00 39.03 4.35
1674 2041 7.571613 GCGTAGATATCAACTATCAACTCTCGT 60.572 40.741 5.32 0.00 39.03 4.18
1675 2042 6.739100 GCGTAGATATCAACTATCAACTCTCG 59.261 42.308 5.32 0.00 39.03 4.04
1676 2043 7.585867 TGCGTAGATATCAACTATCAACTCTC 58.414 38.462 5.32 0.00 39.03 3.20
1677 2044 7.445707 TCTGCGTAGATATCAACTATCAACTCT 59.554 37.037 5.32 0.00 39.03 3.24
1678 2045 7.585867 TCTGCGTAGATATCAACTATCAACTC 58.414 38.462 5.32 0.00 39.03 3.01
1679 2046 7.511959 TCTGCGTAGATATCAACTATCAACT 57.488 36.000 5.32 0.00 39.03 3.16
1680 2047 8.240682 AGATCTGCGTAGATATCAACTATCAAC 58.759 37.037 16.42 0.00 43.63 3.18
1681 2048 8.341892 AGATCTGCGTAGATATCAACTATCAA 57.658 34.615 16.42 0.00 43.63 2.57
1682 2049 7.929941 AGATCTGCGTAGATATCAACTATCA 57.070 36.000 16.42 0.00 43.63 2.15
1683 2050 9.632807 AAAAGATCTGCGTAGATATCAACTATC 57.367 33.333 16.42 1.51 43.63 2.08
1684 2051 9.416794 CAAAAGATCTGCGTAGATATCAACTAT 57.583 33.333 16.42 0.00 43.63 2.12
1685 2052 8.414003 ACAAAAGATCTGCGTAGATATCAACTA 58.586 33.333 16.42 0.00 43.63 2.24
1686 2053 7.268586 ACAAAAGATCTGCGTAGATATCAACT 58.731 34.615 16.42 5.95 43.63 3.16
1687 2054 7.470289 ACAAAAGATCTGCGTAGATATCAAC 57.530 36.000 16.42 3.60 43.63 3.18
1688 2055 9.196552 CATACAAAAGATCTGCGTAGATATCAA 57.803 33.333 16.42 0.00 43.63 2.57
1689 2056 8.576442 TCATACAAAAGATCTGCGTAGATATCA 58.424 33.333 16.42 0.00 43.63 2.15
1690 2057 8.972262 TCATACAAAAGATCTGCGTAGATATC 57.028 34.615 16.42 6.01 43.63 1.63
1691 2058 9.416794 CTTCATACAAAAGATCTGCGTAGATAT 57.583 33.333 16.42 10.62 43.63 1.63
1692 2059 7.382488 GCTTCATACAAAAGATCTGCGTAGATA 59.618 37.037 16.42 0.00 43.63 1.98
1693 2060 6.201806 GCTTCATACAAAAGATCTGCGTAGAT 59.798 38.462 16.40 16.40 46.22 1.98
1694 2061 5.520288 GCTTCATACAAAAGATCTGCGTAGA 59.480 40.000 5.45 5.45 37.35 2.59
1695 2062 5.555256 CGCTTCATACAAAAGATCTGCGTAG 60.555 44.000 0.00 0.00 35.82 3.51
1696 2063 4.267690 CGCTTCATACAAAAGATCTGCGTA 59.732 41.667 0.00 0.00 35.82 4.42
1697 2064 3.062639 CGCTTCATACAAAAGATCTGCGT 59.937 43.478 0.00 0.00 35.82 5.24
1698 2065 3.306973 TCGCTTCATACAAAAGATCTGCG 59.693 43.478 9.65 9.65 40.81 5.18
1699 2066 4.864916 TCGCTTCATACAAAAGATCTGC 57.135 40.909 0.00 0.00 0.00 4.26
1700 2067 5.007430 AGCATCGCTTCATACAAAAGATCTG 59.993 40.000 0.00 0.00 33.89 2.90
1701 2068 5.121811 AGCATCGCTTCATACAAAAGATCT 58.878 37.500 0.00 0.00 33.89 2.75
1702 2069 5.415415 AGCATCGCTTCATACAAAAGATC 57.585 39.130 0.00 0.00 33.89 2.75
1703 2070 6.051717 AGTAGCATCGCTTCATACAAAAGAT 58.948 36.000 0.00 0.00 40.44 2.40
1704 2071 5.419542 AGTAGCATCGCTTCATACAAAAGA 58.580 37.500 0.00 0.00 40.44 2.52
1705 2072 5.725110 AGTAGCATCGCTTCATACAAAAG 57.275 39.130 0.00 0.00 40.44 2.27
1706 2073 5.641636 TGAAGTAGCATCGCTTCATACAAAA 59.358 36.000 3.24 0.00 44.01 2.44
1707 2074 5.175127 TGAAGTAGCATCGCTTCATACAAA 58.825 37.500 3.24 0.00 44.01 2.83
1708 2075 4.754322 TGAAGTAGCATCGCTTCATACAA 58.246 39.130 3.24 0.00 44.01 2.41
1709 2076 4.385358 TGAAGTAGCATCGCTTCATACA 57.615 40.909 3.24 0.00 44.01 2.29
1713 2080 2.995939 CAAGTGAAGTAGCATCGCTTCA 59.004 45.455 3.24 3.24 43.70 3.02
1714 2081 2.996621 ACAAGTGAAGTAGCATCGCTTC 59.003 45.455 0.00 0.00 43.70 3.86
1715 2082 2.738846 CACAAGTGAAGTAGCATCGCTT 59.261 45.455 0.00 0.00 45.76 4.68
1716 2083 2.341257 CACAAGTGAAGTAGCATCGCT 58.659 47.619 0.00 0.00 43.41 4.93
1717 2084 1.201965 GCACAAGTGAAGTAGCATCGC 60.202 52.381 4.04 0.00 0.00 4.58
1718 2085 1.394917 GGCACAAGTGAAGTAGCATCG 59.605 52.381 4.04 0.00 0.00 3.84
1719 2086 2.417933 CAGGCACAAGTGAAGTAGCATC 59.582 50.000 4.04 0.00 0.00 3.91
1720 2087 2.430465 CAGGCACAAGTGAAGTAGCAT 58.570 47.619 4.04 0.00 0.00 3.79
1721 2088 1.882912 CAGGCACAAGTGAAGTAGCA 58.117 50.000 4.04 0.00 0.00 3.49
1722 2089 0.519077 GCAGGCACAAGTGAAGTAGC 59.481 55.000 4.04 0.00 0.00 3.58
1723 2090 1.802960 CTGCAGGCACAAGTGAAGTAG 59.197 52.381 5.57 0.00 0.00 2.57
1724 2091 1.543208 CCTGCAGGCACAAGTGAAGTA 60.543 52.381 22.33 0.00 0.00 2.24
1725 2092 0.820891 CCTGCAGGCACAAGTGAAGT 60.821 55.000 22.33 0.00 0.00 3.01
1726 2093 1.521450 CCCTGCAGGCACAAGTGAAG 61.521 60.000 28.39 5.53 0.00 3.02
1727 2094 1.529010 CCCTGCAGGCACAAGTGAA 60.529 57.895 28.39 0.00 0.00 3.18
1728 2095 2.113774 CCCTGCAGGCACAAGTGA 59.886 61.111 28.39 0.00 0.00 3.41
1729 2096 2.203394 ACCCTGCAGGCACAAGTG 60.203 61.111 28.39 14.16 40.58 3.16
1730 2097 2.203394 CACCCTGCAGGCACAAGT 60.203 61.111 28.39 16.41 40.58 3.16
1731 2098 2.203394 ACACCCTGCAGGCACAAG 60.203 61.111 28.39 15.70 40.58 3.16
1732 2099 2.203337 GACACCCTGCAGGCACAA 60.203 61.111 28.39 0.00 40.58 3.33
1733 2100 4.624364 CGACACCCTGCAGGCACA 62.624 66.667 28.39 0.00 40.58 4.57
1734 2101 4.626081 ACGACACCCTGCAGGCAC 62.626 66.667 28.39 15.55 40.58 5.01
1735 2102 4.624364 CACGACACCCTGCAGGCA 62.624 66.667 28.39 0.00 40.58 4.75
1738 2105 4.624364 TGGCACGACACCCTGCAG 62.624 66.667 6.78 6.78 34.90 4.41
1739 2106 4.624364 CTGGCACGACACCCTGCA 62.624 66.667 0.00 0.00 34.90 4.41
1740 2107 3.825160 TTCTGGCACGACACCCTGC 62.825 63.158 0.00 0.00 0.00 4.85
1741 2108 1.669115 CTTCTGGCACGACACCCTG 60.669 63.158 0.00 0.00 0.00 4.45
1742 2109 2.743718 CTTCTGGCACGACACCCT 59.256 61.111 0.00 0.00 0.00 4.34
1743 2110 3.050275 GCTTCTGGCACGACACCC 61.050 66.667 0.00 0.00 41.35 4.61
2041 2408 5.358922 TCCTCTAGACGCTAGTAGAAGTTC 58.641 45.833 0.00 0.00 0.00 3.01
2061 2428 3.491619 CGATCGACTGGTTTGATGATCCT 60.492 47.826 10.26 0.00 30.92 3.24
2077 2444 0.179197 GAAGCAGTGTCGTCGATCGA 60.179 55.000 15.15 15.15 46.83 3.59
2078 2445 0.179187 AGAAGCAGTGTCGTCGATCG 60.179 55.000 9.36 9.36 41.41 3.69
2079 2446 1.983972 AAGAAGCAGTGTCGTCGATC 58.016 50.000 0.00 0.00 0.00 3.69
2127 2500 6.442112 AGGGCGTCTTACGATTTAGTAATAC 58.558 40.000 3.22 0.00 46.05 1.89
2130 2503 4.641989 AGAGGGCGTCTTACGATTTAGTAA 59.358 41.667 3.41 0.00 46.05 2.24
2131 2504 4.036027 CAGAGGGCGTCTTACGATTTAGTA 59.964 45.833 7.04 0.00 46.05 1.82
2137 2510 1.135083 CAACAGAGGGCGTCTTACGAT 60.135 52.381 7.04 0.00 46.05 3.73
2138 2511 0.242825 CAACAGAGGGCGTCTTACGA 59.757 55.000 7.04 0.00 46.05 3.43
2139 2512 1.352156 GCAACAGAGGGCGTCTTACG 61.352 60.000 7.04 0.00 45.88 3.18
2189 2567 7.336931 AGTGCCTCTAAAACATGAACGAATAAT 59.663 33.333 0.00 0.00 0.00 1.28
2190 2568 6.653320 AGTGCCTCTAAAACATGAACGAATAA 59.347 34.615 0.00 0.00 0.00 1.40
2191 2569 6.170506 AGTGCCTCTAAAACATGAACGAATA 58.829 36.000 0.00 0.00 0.00 1.75
2208 2586 1.803555 GTGCAAGAAAGAGAGTGCCTC 59.196 52.381 0.00 0.00 42.28 4.70
2210 2588 0.877743 GGTGCAAGAAAGAGAGTGCC 59.122 55.000 0.00 0.00 36.12 5.01
2215 2620 4.623932 ATGTGTAGGTGCAAGAAAGAGA 57.376 40.909 0.00 0.00 0.00 3.10
2254 2659 0.175302 TTGTGTGCTTGCCTGGTTTG 59.825 50.000 0.00 0.00 0.00 2.93
2330 2748 4.107051 GCGTGCTGCAAATCCGCT 62.107 61.111 22.72 0.00 45.45 5.52
2452 2872 1.667724 GCCCTCATCACAAGAATCACG 59.332 52.381 0.00 0.00 0.00 4.35
2513 2960 6.205658 TCGATTGTTGTCATACCATGTTTCAA 59.794 34.615 0.00 0.00 0.00 2.69
2520 2967 6.429692 TGAAACTTCGATTGTTGTCATACCAT 59.570 34.615 5.30 0.00 0.00 3.55
2532 2979 5.455525 GTGTTGGTTCTTGAAACTTCGATTG 59.544 40.000 0.00 0.00 0.00 2.67
2537 2984 8.644619 GTTTTAAGTGTTGGTTCTTGAAACTTC 58.355 33.333 13.81 0.00 41.96 3.01
2597 3044 0.806102 CCGATTGCCTCGTGATTCGT 60.806 55.000 5.24 0.00 46.18 3.85
2735 3189 1.522668 TGCTTTCCCAAGTGACGATG 58.477 50.000 0.00 0.00 31.86 3.84
2736 3190 1.880027 GTTGCTTTCCCAAGTGACGAT 59.120 47.619 0.00 0.00 31.86 3.73
2797 3252 2.300433 GTCATATGTCCAATGGCAGCA 58.700 47.619 1.90 0.00 0.00 4.41
2830 3285 3.848978 ACCAACTTCTAGGGTAGGAGT 57.151 47.619 0.00 0.00 46.59 3.85
2846 3301 1.596934 CTCAAGCTCCGCCTACCAA 59.403 57.895 0.00 0.00 0.00 3.67
2895 3350 1.230635 AAGCAAGTCGCACGCTCATT 61.231 50.000 0.00 0.00 46.13 2.57
2921 3376 2.073776 AGGAAACCACCTCATCCCTTT 58.926 47.619 0.00 0.00 34.98 3.11
3032 3487 3.314331 CACAGGCCTGGACCGACT 61.314 66.667 35.42 11.03 34.19 4.18


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

AutoCloner maintained by Alex Coulton.