Multiple sequence alignment - TraesCS2A01G531200

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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 TraesCS2A01G531200 chr2A 100.000 2273 0 0 1 2273 748523468 748525740 0.000000e+00 4198.0
1 TraesCS2A01G531200 chr2A 87.336 458 32 12 1766 2223 739440462 739440031 3.370000e-138 501.0
2 TraesCS2A01G531200 chr2A 85.911 291 28 8 974 1260 748558285 748558566 4.750000e-77 298.0
3 TraesCS2A01G531200 chr5A 94.722 701 21 1 1 685 672025141 672025841 0.000000e+00 1075.0
4 TraesCS2A01G531200 chr2D 87.052 1004 59 18 681 1645 617991852 617992823 0.000000e+00 1068.0
5 TraesCS2A01G531200 chr2D 79.053 549 73 32 736 1260 587112084 587111554 2.800000e-89 339.0
6 TraesCS2A01G531200 chr2D 87.640 267 27 4 1001 1261 617957700 617957966 2.840000e-79 305.0
7 TraesCS2A01G531200 chr2D 87.833 263 29 3 1001 1260 618132569 618132831 2.840000e-79 305.0
8 TraesCS2A01G531200 chr2D 87.452 263 30 2 1001 1260 617973052 617973314 1.320000e-77 300.0
9 TraesCS2A01G531200 chr2D 86.282 277 33 4 988 1261 617941876 617942150 1.710000e-76 296.0
10 TraesCS2A01G531200 chr2D 89.241 158 14 1 1107 1261 617536160 617536317 6.410000e-46 195.0
11 TraesCS2A01G531200 chr2D 96.629 89 2 1 1640 1727 617993034 617993122 1.820000e-31 147.0
12 TraesCS2A01G531200 chr3B 92.960 696 33 5 1 683 823510254 823510946 0.000000e+00 1000.0
13 TraesCS2A01G531200 chr2B 92.847 699 33 6 1 683 799411039 799411736 0.000000e+00 998.0
14 TraesCS2A01G531200 chr2B 85.860 983 82 17 681 1624 753973780 753974744 0.000000e+00 992.0
15 TraesCS2A01G531200 chr2B 91.991 462 35 2 1760 2221 162506010 162505551 0.000000e+00 647.0
16 TraesCS2A01G531200 chr2B 88.768 276 26 3 988 1260 708863278 708863005 1.300000e-87 333.0
17 TraesCS2A01G531200 chr1B 92.539 697 35 7 1 683 28491899 28492592 0.000000e+00 983.0
18 TraesCS2A01G531200 chr1B 91.714 700 40 4 1 683 656573105 656572407 0.000000e+00 955.0
19 TraesCS2A01G531200 chr1B 93.059 461 31 1 1763 2223 642040682 642040223 0.000000e+00 673.0
20 TraesCS2A01G531200 chr4A 92.286 700 34 5 1 683 573894477 573893781 0.000000e+00 976.0
21 TraesCS2A01G531200 chr4A 93.115 305 19 2 380 683 665507114 665507417 1.600000e-121 446.0
22 TraesCS2A01G531200 chr6B 92.068 706 35 5 1 687 654179549 654180252 0.000000e+00 974.0
23 TraesCS2A01G531200 chr6B 93.416 486 16 2 1 471 664630771 664631255 0.000000e+00 706.0
24 TraesCS2A01G531200 chr6B 90.611 458 40 3 1766 2223 620872642 620872188 2.500000e-169 604.0
25 TraesCS2A01G531200 chr4B 91.869 701 38 4 1 685 166768099 166767402 0.000000e+00 961.0
26 TraesCS2A01G531200 chr1D 90.393 687 43 14 1 685 65079750 65079085 0.000000e+00 881.0
27 TraesCS2A01G531200 chr1D 88.269 699 49 13 1 683 226833832 226833151 0.000000e+00 806.0
28 TraesCS2A01G531200 chr1D 91.361 463 35 3 1763 2223 465020079 465019620 1.480000e-176 628.0
29 TraesCS2A01G531200 chr1D 88.018 217 24 1 1763 1979 450745799 450746013 2.900000e-64 255.0
30 TraesCS2A01G531200 chr1D 95.302 149 7 0 2030 2178 450746019 450746167 1.050000e-58 237.0
31 TraesCS2A01G531200 chr1D 94.828 58 3 0 2216 2273 450746381 450746438 8.650000e-15 91.6
32 TraesCS2A01G531200 chr6D 88.478 703 48 12 1 685 31845675 31844988 0.000000e+00 819.0
33 TraesCS2A01G531200 chr6D 85.542 83 12 0 1020 1102 88832009 88832091 1.120000e-13 87.9
34 TraesCS2A01G531200 chr5B 90.393 458 35 4 1766 2223 527950722 527950274 5.410000e-166 593.0
35 TraesCS2A01G531200 chr5B 89.421 397 25 3 304 684 368714639 368714244 3.390000e-133 484.0
36 TraesCS2A01G531200 chr7A 91.832 404 31 2 1759 2161 8649539 8649941 1.520000e-156 562.0
37 TraesCS2A01G531200 chr7A 91.123 383 32 2 1764 2146 236328188 236327808 3.350000e-143 518.0
38 TraesCS2A01G531200 chr7A 98.077 52 1 0 2222 2273 8650020 8650071 8.650000e-15 91.6
39 TraesCS2A01G531200 chr7A 91.228 57 5 0 2217 2273 236327470 236327414 6.730000e-11 78.7


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 TraesCS2A01G531200 chr2A 748523468 748525740 2272 False 4198.00 4198 100.0000 1 2273 1 chr2A.!!$F1 2272
1 TraesCS2A01G531200 chr5A 672025141 672025841 700 False 1075.00 1075 94.7220 1 685 1 chr5A.!!$F1 684
2 TraesCS2A01G531200 chr2D 617991852 617993122 1270 False 607.50 1068 91.8405 681 1727 2 chr2D.!!$F6 1046
3 TraesCS2A01G531200 chr2D 587111554 587112084 530 True 339.00 339 79.0530 736 1260 1 chr2D.!!$R1 524
4 TraesCS2A01G531200 chr3B 823510254 823510946 692 False 1000.00 1000 92.9600 1 683 1 chr3B.!!$F1 682
5 TraesCS2A01G531200 chr2B 799411039 799411736 697 False 998.00 998 92.8470 1 683 1 chr2B.!!$F2 682
6 TraesCS2A01G531200 chr2B 753973780 753974744 964 False 992.00 992 85.8600 681 1624 1 chr2B.!!$F1 943
7 TraesCS2A01G531200 chr1B 28491899 28492592 693 False 983.00 983 92.5390 1 683 1 chr1B.!!$F1 682
8 TraesCS2A01G531200 chr1B 656572407 656573105 698 True 955.00 955 91.7140 1 683 1 chr1B.!!$R2 682
9 TraesCS2A01G531200 chr4A 573893781 573894477 696 True 976.00 976 92.2860 1 683 1 chr4A.!!$R1 682
10 TraesCS2A01G531200 chr6B 654179549 654180252 703 False 974.00 974 92.0680 1 687 1 chr6B.!!$F1 686
11 TraesCS2A01G531200 chr4B 166767402 166768099 697 True 961.00 961 91.8690 1 685 1 chr4B.!!$R1 684
12 TraesCS2A01G531200 chr1D 65079085 65079750 665 True 881.00 881 90.3930 1 685 1 chr1D.!!$R1 684
13 TraesCS2A01G531200 chr1D 226833151 226833832 681 True 806.00 806 88.2690 1 683 1 chr1D.!!$R2 682
14 TraesCS2A01G531200 chr6D 31844988 31845675 687 True 819.00 819 88.4780 1 685 1 chr6D.!!$R1 684
15 TraesCS2A01G531200 chr7A 8649539 8650071 532 False 326.80 562 94.9545 1759 2273 2 chr7A.!!$F1 514
16 TraesCS2A01G531200 chr7A 236327414 236328188 774 True 298.35 518 91.1755 1764 2273 2 chr7A.!!$R1 509

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
940 1000 0.321122 CACAGAGTTCAGGCAGACCC 60.321 60.0 0.0 0.0 36.11 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 2093 0.109597 CTCCTTTCAACGCCACATGC 60.11 55.0 0.0 0.0 0.0 4.06 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
239 242 6.499106 AAAACTTGTTGGAGGGATTGAAAT 57.501 33.333 0.00 0.00 0.00 2.17
260 263 9.052759 TGAAATAGCTTACTTTTCTTTCTTCGT 57.947 29.630 0.00 0.00 32.02 3.85
336 345 3.157949 GGGGAAGAGAGAGGGCGG 61.158 72.222 0.00 0.00 0.00 6.13
435 462 2.758737 CCCTACCGCCGGAGTCTT 60.759 66.667 11.71 0.00 0.00 3.01
468 495 3.654173 GACAACCTACCGCCGGGTC 62.654 68.421 8.57 0.00 46.01 4.46
688 717 0.389687 CACGAAATTTTGCCGCCCAT 60.390 50.000 5.27 0.00 0.00 4.00
750 779 4.080807 TGAATTCTGAAAGCACCCGGTATA 60.081 41.667 7.05 0.00 0.00 1.47
768 797 2.259266 TACTGGAAAACCAACGTCCC 57.741 50.000 0.00 0.00 0.00 4.46
786 815 0.404040 CCCTGCCACCTGTTTTCCTA 59.596 55.000 0.00 0.00 0.00 2.94
823 862 1.833787 TAACACCTTCGGCTCCCACC 61.834 60.000 0.00 0.00 0.00 4.61
863 914 4.948257 AGCATCGATCAGCTTGCA 57.052 50.000 8.43 0.00 38.01 4.08
864 915 2.691571 AGCATCGATCAGCTTGCAG 58.308 52.632 8.43 0.00 38.01 4.41
865 916 1.009900 GCATCGATCAGCTTGCAGC 60.010 57.895 0.00 0.47 42.84 5.25
891 945 3.221771 CTCCTTCACCACCACAAAATCA 58.778 45.455 0.00 0.00 0.00 2.57
940 1000 0.321122 CACAGAGTTCAGGCAGACCC 60.321 60.000 0.00 0.00 36.11 4.46
996 1056 3.831333 AGAACAGAGTTGCAGAGAGATCA 59.169 43.478 0.00 0.00 0.00 2.92
997 1057 4.467082 AGAACAGAGTTGCAGAGAGATCAT 59.533 41.667 0.00 0.00 0.00 2.45
998 1058 4.126208 ACAGAGTTGCAGAGAGATCATG 57.874 45.455 0.00 0.00 0.00 3.07
999 1059 3.768215 ACAGAGTTGCAGAGAGATCATGA 59.232 43.478 0.00 0.00 0.00 3.07
1013 1073 2.048023 CATGAATGGCAGGTGCGGT 61.048 57.895 0.00 0.00 43.26 5.68
1017 1077 1.523154 GAATGGCAGGTGCGGTGAAA 61.523 55.000 0.00 0.00 43.26 2.69
1113 1173 2.507944 GCGCTCAGGTCCATCCAT 59.492 61.111 0.00 0.00 39.02 3.41
1116 1176 1.826024 GCTCAGGTCCATCCATCGT 59.174 57.895 0.00 0.00 39.02 3.73
1130 1190 3.866379 ATCGTGCAGCCAAGGCCAA 62.866 57.895 5.01 0.00 43.17 4.52
1131 1191 3.604667 CGTGCAGCCAAGGCCAAA 61.605 61.111 5.01 0.00 43.17 3.28
1300 1393 2.937433 GCTCCAGCCTCTGTTAGAAACC 60.937 54.545 0.00 0.00 34.31 3.27
1352 1458 5.637810 CCTGCCGATTGTAAATACGTATCAT 59.362 40.000 8.86 3.86 0.00 2.45
1370 1476 8.204836 ACGTATCATGATGATGATGATGATGAT 58.795 33.333 18.72 10.95 46.83 2.45
1371 1477 9.692749 CGTATCATGATGATGATGATGATGATA 57.307 33.333 18.72 9.23 46.83 2.15
1395 1501 3.117322 TGATGAAACCTTTCCCCACTTCA 60.117 43.478 0.00 0.00 36.36 3.02
1478 1584 9.541143 TTGTTTCAAATTCTTTGGGAAGATTAC 57.459 29.630 0.19 0.00 41.35 1.89
1494 1600 2.623878 TTACTGTTTCGAGTTGGGCA 57.376 45.000 0.00 0.00 0.00 5.36
1548 1672 1.567649 AGCATTGATCCTGGTCCACAT 59.432 47.619 0.00 0.00 0.00 3.21
1568 1693 1.681538 TTTTCCGCCAGCTTGTACAA 58.318 45.000 8.28 8.28 0.00 2.41
1618 1746 5.029014 CGAATTAGTCTCGTAGGTTCAGTG 58.971 45.833 0.00 0.00 0.00 3.66
1624 1752 6.680874 AGTCTCGTAGGTTCAGTGTTATAG 57.319 41.667 0.00 0.00 0.00 1.31
1626 1754 7.055378 AGTCTCGTAGGTTCAGTGTTATAGAT 58.945 38.462 0.00 0.00 0.00 1.98
1666 2010 7.928706 AGTACAGTATGCATCTTTCCACTATTC 59.071 37.037 0.19 0.00 42.53 1.75
1729 2074 1.886037 CGTACGCGTGACTGTTATCA 58.114 50.000 24.59 0.00 0.00 2.15
1730 2075 2.244251 CGTACGCGTGACTGTTATCAA 58.756 47.619 24.59 0.00 0.00 2.57
1731 2076 2.850060 CGTACGCGTGACTGTTATCAAT 59.150 45.455 24.59 0.00 0.00 2.57
1732 2077 3.062059 CGTACGCGTGACTGTTATCAATC 60.062 47.826 24.59 0.00 0.00 2.67
1733 2078 1.917955 ACGCGTGACTGTTATCAATCG 59.082 47.619 12.93 0.00 34.01 3.34
1734 2079 2.182014 CGCGTGACTGTTATCAATCGA 58.818 47.619 0.00 0.00 31.21 3.59
1735 2080 2.214244 CGCGTGACTGTTATCAATCGAG 59.786 50.000 0.00 0.00 31.21 4.04
1736 2081 2.034507 GCGTGACTGTTATCAATCGAGC 60.035 50.000 0.00 0.00 0.00 5.03
1737 2082 2.214244 CGTGACTGTTATCAATCGAGCG 59.786 50.000 0.00 0.00 0.00 5.03
1738 2083 2.034507 GTGACTGTTATCAATCGAGCGC 60.035 50.000 0.00 0.00 0.00 5.92
1739 2084 2.193447 GACTGTTATCAATCGAGCGCA 58.807 47.619 11.47 0.00 0.00 6.09
1740 2085 2.797156 GACTGTTATCAATCGAGCGCAT 59.203 45.455 11.47 0.00 0.00 4.73
1741 2086 3.977427 ACTGTTATCAATCGAGCGCATA 58.023 40.909 11.47 0.00 0.00 3.14
1742 2087 4.368315 ACTGTTATCAATCGAGCGCATAA 58.632 39.130 11.47 0.00 0.00 1.90
1743 2088 4.808895 ACTGTTATCAATCGAGCGCATAAA 59.191 37.500 11.47 0.00 0.00 1.40
1744 2089 5.466728 ACTGTTATCAATCGAGCGCATAAAT 59.533 36.000 11.47 0.00 0.00 1.40
1745 2090 5.678921 TGTTATCAATCGAGCGCATAAATG 58.321 37.500 11.47 2.85 0.00 2.32
1746 2091 5.465056 TGTTATCAATCGAGCGCATAAATGA 59.535 36.000 11.47 9.00 0.00 2.57
1747 2092 6.018343 TGTTATCAATCGAGCGCATAAATGAA 60.018 34.615 11.47 0.00 0.00 2.57
1748 2093 4.457433 TCAATCGAGCGCATAAATGAAG 57.543 40.909 11.47 0.00 0.00 3.02
1749 2094 2.957576 ATCGAGCGCATAAATGAAGC 57.042 45.000 11.47 0.00 34.63 3.86
1750 2095 1.650825 TCGAGCGCATAAATGAAGCA 58.349 45.000 11.47 0.00 36.10 3.91
1751 2096 2.212652 TCGAGCGCATAAATGAAGCAT 58.787 42.857 11.47 0.00 36.10 3.79
1752 2097 2.032636 TCGAGCGCATAAATGAAGCATG 60.033 45.455 11.47 0.00 36.10 4.06
1753 2098 2.286595 CGAGCGCATAAATGAAGCATGT 60.287 45.455 11.47 0.00 36.10 3.21
1754 2099 3.040795 GAGCGCATAAATGAAGCATGTG 58.959 45.455 11.47 0.00 36.10 3.21
1755 2100 2.121786 GCGCATAAATGAAGCATGTGG 58.878 47.619 0.30 0.00 34.59 4.17
1756 2101 2.121786 CGCATAAATGAAGCATGTGGC 58.878 47.619 0.00 0.00 45.30 5.01
1776 2121 5.049267 GTGGCGTTGAAAGGAGTATTTAACA 60.049 40.000 0.00 0.00 0.00 2.41
1806 2151 2.019249 CACAATTCATGGATCCGTGCT 58.981 47.619 26.64 14.69 33.28 4.40
1809 2154 2.882761 CAATTCATGGATCCGTGCTCAT 59.117 45.455 26.64 15.89 33.28 2.90
1816 2161 4.955811 TGGATCCGTGCTCATAAACTAT 57.044 40.909 7.39 0.00 0.00 2.12
1824 2169 7.497595 TCCGTGCTCATAAACTATCACTTTAT 58.502 34.615 0.00 0.00 0.00 1.40
1836 2181 7.701539 ACTATCACTTTATGAATTTGTGCCA 57.298 32.000 0.00 0.00 41.93 4.92
1850 2195 4.810191 TTGTGCCAAAAACTACCACTTT 57.190 36.364 0.00 0.00 0.00 2.66
1953 2298 3.517901 TCCGGGATGAAATAGTCAACACT 59.482 43.478 0.00 0.00 40.50 3.55
1974 2319 3.199677 TGTTACTTTGACCGTCAACCTG 58.800 45.455 13.61 9.41 35.89 4.00
1994 2339 0.844661 AGGGGCCCACATGTCAGTTA 60.845 55.000 27.72 0.00 0.00 2.24
2162 2508 3.455469 GCCATGGCCAGCTCAACC 61.455 66.667 27.24 0.00 34.56 3.77
2163 2509 2.757099 CCATGGCCAGCTCAACCC 60.757 66.667 13.05 0.00 0.00 4.11
2164 2510 2.757099 CATGGCCAGCTCAACCCC 60.757 66.667 13.05 0.00 0.00 4.95
2166 2512 1.619363 ATGGCCAGCTCAACCCCTA 60.619 57.895 13.05 0.00 0.00 3.53
2167 2513 1.639635 ATGGCCAGCTCAACCCCTAG 61.640 60.000 13.05 0.00 0.00 3.02
2168 2514 2.592308 GCCAGCTCAACCCCTAGG 59.408 66.667 0.06 0.06 40.04 3.02
2169 2515 1.995626 GCCAGCTCAACCCCTAGGA 60.996 63.158 11.48 0.00 36.73 2.94
2171 2517 0.909610 CCAGCTCAACCCCTAGGACA 60.910 60.000 11.48 0.00 36.73 4.02
2172 2518 0.250513 CAGCTCAACCCCTAGGACAC 59.749 60.000 11.48 0.00 36.73 3.67
2173 2519 0.117340 AGCTCAACCCCTAGGACACT 59.883 55.000 11.48 0.00 36.73 3.55
2175 2521 1.757699 GCTCAACCCCTAGGACACTAG 59.242 57.143 11.48 3.21 45.13 2.57
2183 2529 3.097461 TAGGACACTAGAGCCTCGC 57.903 57.895 0.00 0.00 33.28 5.03
2184 2530 0.465824 TAGGACACTAGAGCCTCGCC 60.466 60.000 0.00 0.00 33.28 5.54
2185 2531 2.409651 GACACTAGAGCCTCGCCG 59.590 66.667 0.00 0.00 0.00 6.46
2186 2532 3.127352 GACACTAGAGCCTCGCCGG 62.127 68.421 0.00 0.00 0.00 6.13
2187 2533 3.141488 CACTAGAGCCTCGCCGGT 61.141 66.667 1.90 0.00 34.25 5.28
2188 2534 3.141488 ACTAGAGCCTCGCCGGTG 61.141 66.667 9.28 9.28 34.25 4.94
2189 2535 2.829003 CTAGAGCCTCGCCGGTGA 60.829 66.667 18.43 18.43 34.25 4.02
2190 2536 2.829003 TAGAGCCTCGCCGGTGAG 60.829 66.667 33.64 33.64 35.70 3.51
2196 2542 4.200283 CTCGCCGGTGAGCTCCTC 62.200 72.222 30.71 4.30 0.00 3.71
2198 2544 3.764466 CGCCGGTGAGCTCCTCTT 61.764 66.667 10.20 0.00 0.00 2.85
2199 2545 2.185608 GCCGGTGAGCTCCTCTTC 59.814 66.667 12.15 0.00 0.00 2.87
2201 2547 1.684049 CCGGTGAGCTCCTCTTCCT 60.684 63.158 12.15 0.00 0.00 3.36
2202 2548 1.671901 CCGGTGAGCTCCTCTTCCTC 61.672 65.000 12.15 0.00 0.00 3.71
2204 2550 0.823460 GGTGAGCTCCTCTTCCTCTG 59.177 60.000 12.15 0.00 0.00 3.35
2205 2551 0.175531 GTGAGCTCCTCTTCCTCTGC 59.824 60.000 12.15 0.00 0.00 4.26
2206 2552 0.975040 TGAGCTCCTCTTCCTCTGCC 60.975 60.000 12.15 0.00 0.00 4.85
2207 2553 2.015227 GAGCTCCTCTTCCTCTGCCG 62.015 65.000 0.87 0.00 0.00 5.69
2209 2555 1.813192 CTCCTCTTCCTCTGCCGTC 59.187 63.158 0.00 0.00 0.00 4.79
2210 2556 1.999071 CTCCTCTTCCTCTGCCGTCG 61.999 65.000 0.00 0.00 0.00 5.12
2211 2557 2.202676 CTCTTCCTCTGCCGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 162 8.335532 TCGTTTGAAATCACTCCTATTTGAAT 57.664 30.769 0.00 0.00 0.00 2.57
239 242 5.178809 GCCACGAAGAAAGAAAAGTAAGCTA 59.821 40.000 0.00 0.00 0.00 3.32
260 263 2.250741 TTTGCGGATCGAGATGGCCA 62.251 55.000 8.56 8.56 0.00 5.36
435 462 1.180456 TTGTCTGAACCTACCGCCGA 61.180 55.000 0.00 0.00 0.00 5.54
688 717 2.970324 GCTGTCGTTCCGGTGCAA 60.970 61.111 0.00 0.00 0.00 4.08
768 797 2.094675 CATAGGAAAACAGGTGGCAGG 58.905 52.381 0.00 0.00 0.00 4.85
786 815 2.570302 GTTATATACACGGGAGGGCCAT 59.430 50.000 6.18 0.00 35.95 4.40
811 850 1.838073 GAAGAAGGGTGGGAGCCGAA 61.838 60.000 0.00 0.00 41.56 4.30
823 862 5.756195 TGTTTGTGTTGATGAGAAGAAGG 57.244 39.130 0.00 0.00 0.00 3.46
863 914 1.676384 GTGGTGAAGGAGCTGAGCT 59.324 57.895 6.69 6.69 43.88 4.09
864 915 1.376553 GGTGGTGAAGGAGCTGAGC 60.377 63.158 0.00 0.00 0.00 4.26
865 916 0.321122 GTGGTGGTGAAGGAGCTGAG 60.321 60.000 0.00 0.00 0.00 3.35
866 917 1.053835 TGTGGTGGTGAAGGAGCTGA 61.054 55.000 0.00 0.00 0.00 4.26
867 918 0.179020 TTGTGGTGGTGAAGGAGCTG 60.179 55.000 0.00 0.00 0.00 4.24
868 919 0.550914 TTTGTGGTGGTGAAGGAGCT 59.449 50.000 0.00 0.00 0.00 4.09
869 920 1.398692 TTTTGTGGTGGTGAAGGAGC 58.601 50.000 0.00 0.00 0.00 4.70
870 921 3.221771 TGATTTTGTGGTGGTGAAGGAG 58.778 45.455 0.00 0.00 0.00 3.69
871 922 3.304911 TGATTTTGTGGTGGTGAAGGA 57.695 42.857 0.00 0.00 0.00 3.36
872 923 3.131933 TGTTGATTTTGTGGTGGTGAAGG 59.868 43.478 0.00 0.00 0.00 3.46
873 924 4.111916 GTGTTGATTTTGTGGTGGTGAAG 58.888 43.478 0.00 0.00 0.00 3.02
891 945 4.833478 AGATTGATAGCAGTGGAGTGTT 57.167 40.909 0.00 0.00 0.00 3.32
940 1000 2.951745 GAGACGATGCCGCTGACG 60.952 66.667 0.00 0.00 39.95 4.35
996 1056 2.048023 CACCGCACCTGCCATTCAT 61.048 57.895 0.00 0.00 37.91 2.57
997 1057 2.672651 CACCGCACCTGCCATTCA 60.673 61.111 0.00 0.00 37.91 2.57
998 1058 1.523154 TTTCACCGCACCTGCCATTC 61.523 55.000 0.00 0.00 37.91 2.67
999 1059 1.526575 CTTTCACCGCACCTGCCATT 61.527 55.000 0.00 0.00 37.91 3.16
1013 1073 1.006825 CACCATCGACGACGCTTTCA 61.007 55.000 0.00 0.00 39.58 2.69
1017 1077 4.796231 GCCACCATCGACGACGCT 62.796 66.667 0.00 0.00 39.58 5.07
1025 1085 3.333189 CGCTCATCGCCACCATCG 61.333 66.667 0.00 0.00 34.21 3.84
1113 1173 4.577677 TTGGCCTTGGCTGCACGA 62.578 61.111 11.71 0.00 0.00 4.35
1116 1176 3.618750 GCTTTGGCCTTGGCTGCA 61.619 61.111 11.71 0.00 0.00 4.41
1150 1210 2.273449 CTTTGCGCCCTGGGAGAT 59.727 61.111 21.55 0.00 0.00 2.75
1300 1393 1.808945 CCAGCCAAGTTGTTGCTAGAG 59.191 52.381 6.34 0.00 31.64 2.43
1370 1476 5.269554 AGTGGGGAAAGGTTTCATCATTA 57.730 39.130 4.89 0.00 38.92 1.90
1371 1477 4.132122 AGTGGGGAAAGGTTTCATCATT 57.868 40.909 4.89 0.00 38.92 2.57
1372 1478 3.833559 AGTGGGGAAAGGTTTCATCAT 57.166 42.857 4.89 0.00 38.92 2.45
1373 1479 3.117322 TGAAGTGGGGAAAGGTTTCATCA 60.117 43.478 4.89 0.00 38.92 3.07
1374 1480 3.496331 TGAAGTGGGGAAAGGTTTCATC 58.504 45.455 4.89 0.00 38.92 2.92
1375 1481 3.611025 TGAAGTGGGGAAAGGTTTCAT 57.389 42.857 4.89 0.00 38.92 2.57
1376 1482 3.295973 CTTGAAGTGGGGAAAGGTTTCA 58.704 45.455 4.89 0.00 38.92 2.69
1377 1483 3.296854 ACTTGAAGTGGGGAAAGGTTTC 58.703 45.455 0.00 0.00 36.46 2.78
1378 1484 3.398318 ACTTGAAGTGGGGAAAGGTTT 57.602 42.857 0.00 0.00 0.00 3.27
1395 1501 5.809001 TCTGAAGCAGGATAATGTGAACTT 58.191 37.500 0.00 0.00 31.51 2.66
1478 1584 1.002468 CTTGTGCCCAACTCGAAACAG 60.002 52.381 0.00 0.00 0.00 3.16
1548 1672 1.681538 TGTACAAGCTGGCGGAAAAA 58.318 45.000 0.00 0.00 0.00 1.94
1641 1769 7.096023 CGAATAGTGGAAAGATGCATACTGTAC 60.096 40.741 0.00 0.00 0.00 2.90
1666 2010 2.116736 AACGCATGTGAGGTTGCACG 62.117 55.000 14.43 0.00 41.63 5.34
1718 2063 2.193447 GCGCTCGATTGATAACAGTCA 58.807 47.619 0.00 0.00 33.31 3.41
1727 2072 3.303329 GCTTCATTTATGCGCTCGATTGA 60.303 43.478 9.73 3.79 0.00 2.57
1728 2073 2.969306 GCTTCATTTATGCGCTCGATTG 59.031 45.455 9.73 1.11 0.00 2.67
1729 2074 2.613595 TGCTTCATTTATGCGCTCGATT 59.386 40.909 9.73 0.00 0.00 3.34
1730 2075 2.212652 TGCTTCATTTATGCGCTCGAT 58.787 42.857 9.73 0.00 0.00 3.59
1731 2076 1.650825 TGCTTCATTTATGCGCTCGA 58.349 45.000 9.73 0.00 0.00 4.04
1732 2077 2.286595 ACATGCTTCATTTATGCGCTCG 60.287 45.455 9.73 0.00 0.00 5.03
1733 2078 3.040795 CACATGCTTCATTTATGCGCTC 58.959 45.455 9.73 0.00 0.00 5.03
1734 2079 2.223641 CCACATGCTTCATTTATGCGCT 60.224 45.455 9.73 0.00 0.00 5.92
1735 2080 2.121786 CCACATGCTTCATTTATGCGC 58.878 47.619 0.00 0.00 0.00 6.09
1736 2081 2.121786 GCCACATGCTTCATTTATGCG 58.878 47.619 0.00 0.00 36.87 4.73
1737 2082 2.121786 CGCCACATGCTTCATTTATGC 58.878 47.619 0.00 0.00 38.05 3.14
1738 2083 3.425577 ACGCCACATGCTTCATTTATG 57.574 42.857 0.00 0.00 38.05 1.90
1739 2084 3.443329 TCAACGCCACATGCTTCATTTAT 59.557 39.130 0.00 0.00 38.05 1.40
1740 2085 2.816672 TCAACGCCACATGCTTCATTTA 59.183 40.909 0.00 0.00 38.05 1.40
1741 2086 1.612950 TCAACGCCACATGCTTCATTT 59.387 42.857 0.00 0.00 38.05 2.32
1742 2087 1.246649 TCAACGCCACATGCTTCATT 58.753 45.000 0.00 0.00 38.05 2.57
1743 2088 1.246649 TTCAACGCCACATGCTTCAT 58.753 45.000 0.00 0.00 38.05 2.57
1744 2089 1.001487 CTTTCAACGCCACATGCTTCA 60.001 47.619 0.00 0.00 38.05 3.02
1745 2090 1.666888 CCTTTCAACGCCACATGCTTC 60.667 52.381 0.00 0.00 38.05 3.86
1746 2091 0.314935 CCTTTCAACGCCACATGCTT 59.685 50.000 0.00 0.00 38.05 3.91
1747 2092 0.537143 TCCTTTCAACGCCACATGCT 60.537 50.000 0.00 0.00 38.05 3.79
1748 2093 0.109597 CTCCTTTCAACGCCACATGC 60.110 55.000 0.00 0.00 0.00 4.06
1749 2094 1.238439 ACTCCTTTCAACGCCACATG 58.762 50.000 0.00 0.00 0.00 3.21
1750 2095 2.851263 TACTCCTTTCAACGCCACAT 57.149 45.000 0.00 0.00 0.00 3.21
1751 2096 2.851263 ATACTCCTTTCAACGCCACA 57.149 45.000 0.00 0.00 0.00 4.17
1752 2097 5.049267 TGTTAAATACTCCTTTCAACGCCAC 60.049 40.000 0.00 0.00 0.00 5.01
1753 2098 5.064558 TGTTAAATACTCCTTTCAACGCCA 58.935 37.500 0.00 0.00 0.00 5.69
1754 2099 5.616488 TGTTAAATACTCCTTTCAACGCC 57.384 39.130 0.00 0.00 0.00 5.68
1755 2100 7.917720 TTTTGTTAAATACTCCTTTCAACGC 57.082 32.000 0.00 0.00 0.00 4.84
1877 2222 9.834628 GTTTAATCGACCATTTTTCATACTTGA 57.165 29.630 0.00 0.00 0.00 3.02
1937 2282 9.337396 TCAAAGTAACAGTGTTGACTATTTCAT 57.663 29.630 18.90 0.44 32.84 2.57
1953 2298 3.118702 TCAGGTTGACGGTCAAAGTAACA 60.119 43.478 23.93 5.01 38.22 2.41
1974 2319 2.142292 AACTGACATGTGGGCCCCTC 62.142 60.000 22.27 13.54 0.00 4.30
1994 2339 4.230964 AGAGGTAGGAGTTGTAGGAGATGT 59.769 45.833 0.00 0.00 0.00 3.06
2158 2504 1.757699 GCTCTAGTGTCCTAGGGGTTG 59.242 57.143 9.46 0.00 41.41 3.77
2159 2505 1.343176 GGCTCTAGTGTCCTAGGGGTT 60.343 57.143 9.46 0.00 41.41 4.11
2160 2506 0.262285 GGCTCTAGTGTCCTAGGGGT 59.738 60.000 9.46 0.00 41.41 4.95
2162 2508 1.816183 CGAGGCTCTAGTGTCCTAGGG 60.816 61.905 13.50 0.00 43.59 3.53
2163 2509 1.600023 CGAGGCTCTAGTGTCCTAGG 58.400 60.000 13.50 0.82 40.98 3.02
2164 2510 0.948678 GCGAGGCTCTAGTGTCCTAG 59.051 60.000 13.50 8.53 41.82 3.02
2166 2512 1.755008 GGCGAGGCTCTAGTGTCCT 60.755 63.158 13.50 7.29 0.00 3.85
2167 2513 2.809010 GGCGAGGCTCTAGTGTCC 59.191 66.667 13.50 0.48 0.00 4.02
2168 2514 2.409651 CGGCGAGGCTCTAGTGTC 59.590 66.667 13.50 0.00 0.00 3.67
2169 2515 3.141488 CCGGCGAGGCTCTAGTGT 61.141 66.667 9.30 0.00 0.00 3.55
2171 2517 3.141488 CACCGGCGAGGCTCTAGT 61.141 66.667 9.30 1.43 46.52 2.57
2172 2518 2.829003 TCACCGGCGAGGCTCTAG 60.829 66.667 9.30 3.45 46.52 2.43
2173 2519 2.829003 CTCACCGGCGAGGCTCTA 60.829 66.667 11.86 0.00 46.52 2.43
2179 2525 4.200283 GAGGAGCTCACCGGCGAG 62.200 72.222 15.36 15.36 37.29 5.03
2180 2526 4.742649 AGAGGAGCTCACCGGCGA 62.743 66.667 17.19 0.00 37.29 5.54
2181 2527 3.708220 GAAGAGGAGCTCACCGGCG 62.708 68.421 17.19 0.00 37.29 6.46
2182 2528 2.185608 GAAGAGGAGCTCACCGGC 59.814 66.667 17.19 0.00 32.06 6.13
2183 2529 1.671901 GAGGAAGAGGAGCTCACCGG 61.672 65.000 17.19 0.00 35.56 5.28
2184 2530 0.682855 AGAGGAAGAGGAGCTCACCG 60.683 60.000 17.19 0.00 35.56 4.94
2185 2531 0.823460 CAGAGGAAGAGGAGCTCACC 59.177 60.000 17.19 10.11 32.06 4.02
2186 2532 0.175531 GCAGAGGAAGAGGAGCTCAC 59.824 60.000 17.19 9.03 32.06 3.51
2187 2533 0.975040 GGCAGAGGAAGAGGAGCTCA 60.975 60.000 17.19 0.00 32.06 4.26
2188 2534 1.822615 GGCAGAGGAAGAGGAGCTC 59.177 63.158 4.71 4.71 0.00 4.09
2189 2535 2.057408 CGGCAGAGGAAGAGGAGCT 61.057 63.158 0.00 0.00 0.00 4.09
2190 2536 2.291457 GACGGCAGAGGAAGAGGAGC 62.291 65.000 0.00 0.00 0.00 4.70
2191 2537 1.813192 GACGGCAGAGGAAGAGGAG 59.187 63.158 0.00 0.00 0.00 3.69
2192 2538 2.046864 CGACGGCAGAGGAAGAGGA 61.047 63.158 0.00 0.00 0.00 3.71
2193 2539 2.492090 CGACGGCAGAGGAAGAGG 59.508 66.667 0.00 0.00 0.00 3.69
2195 2541 2.989253 TGCGACGGCAGAGGAAGA 60.989 61.111 0.00 0.00 46.21 2.87


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

AutoCloner maintained by Alex Coulton.