Multiple sequence alignment - TraesCS3B01G388500

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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 TraesCS3B01G388500 chr3B 100.000 2524 0 0 1 2524 611428663 611426140 0.000000e+00 4662
1 TraesCS3B01G388500 chr3B 93.617 141 7 2 8 146 760588984 760589124 2.540000e-50 209
2 TraesCS3B01G388500 chr3A 88.734 2370 160 45 133 2461 603474168 603471865 0.000000e+00 2798
3 TraesCS3B01G388500 chr3A 83.102 722 65 26 1321 2028 603471870 603471192 2.780000e-169 604
4 TraesCS3B01G388500 chr3D 86.726 2456 178 65 133 2512 461020759 461018376 0.000000e+00 2593
5 TraesCS3B01G388500 chr4B 96.899 129 4 0 8 136 580801726 580801854 1.520000e-52 217
6 TraesCS3B01G388500 chr4B 95.455 132 6 0 7 138 576982569 576982438 7.070000e-51 211
7 TraesCS3B01G388500 chr2B 96.183 131 5 0 8 138 550044053 550044183 5.470000e-52 215
8 TraesCS3B01G388500 chr5D 96.850 127 4 0 8 134 455608055 455607929 1.970000e-51 213
9 TraesCS3B01G388500 chr5B 93.151 146 8 2 8 152 96879069 96878925 1.970000e-51 213
10 TraesCS3B01G388500 chr5B 90.196 153 14 1 8 160 525368966 525369117 5.510000e-47 198
11 TraesCS3B01G388500 chr1D 96.850 127 4 0 8 134 178459638 178459512 1.970000e-51 213
12 TraesCS3B01G388500 chr1B 96.850 127 4 0 8 134 572202439 572202565 1.970000e-51 213


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 TraesCS3B01G388500 chr3B 611426140 611428663 2523 True 4662 4662 100.000 1 2524 1 chr3B.!!$R1 2523
1 TraesCS3B01G388500 chr3A 603471192 603474168 2976 True 1701 2798 85.918 133 2461 2 chr3A.!!$R1 2328
2 TraesCS3B01G388500 chr3D 461018376 461020759 2383 True 2593 2593 86.726 133 2512 1 chr3D.!!$R1 2379

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
20 21 0.754587 ATCGGTTACTCCCTCCGTCC 60.755 60.0 0.0 0.0 43.94 4.79 F
1311 1341 0.325671 AGGGACCTGGACATGATCGT 60.326 55.0 0.0 0.0 0.00 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1446 0.105408 ACCAAACGGCGTACAGAACT 59.895 50.0 15.20 0.0 0.0 3.01 R
2462 2557 2.450609 AGATACGCGAACAACTTGGT 57.549 45.0 15.93 0.0 0.0 3.67 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
18 19 3.294904 AATCGGTTACTCCCTCCGT 57.705 52.632 0.00 0.00 43.94 4.69
19 20 1.109609 AATCGGTTACTCCCTCCGTC 58.890 55.000 0.00 0.00 43.94 4.79
20 21 0.754587 ATCGGTTACTCCCTCCGTCC 60.755 60.000 0.00 0.00 43.94 4.79
21 22 2.768492 CGGTTACTCCCTCCGTCCG 61.768 68.421 0.00 0.00 39.51 4.79
22 23 1.379044 GGTTACTCCCTCCGTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
23 24 0.967380 GGTTACTCCCTCCGTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
24 25 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
25 26 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
26 27 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
27 28 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
28 29 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
29 30 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
30 31 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
31 32 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
32 33 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
33 34 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
34 35 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
35 36 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
36 37 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
37 38 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
38 39 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
39 40 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
40 41 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
41 42 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
42 43 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
43 44 9.490663 GTCCGAAAATACTTGTCATCAAAATAG 57.509 33.333 0.00 0.00 32.87 1.73
44 45 9.443323 TCCGAAAATACTTGTCATCAAAATAGA 57.557 29.630 0.00 0.00 32.87 1.98
99 100 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
105 106 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
108 109 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
109 110 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
110 111 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
111 112 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
112 113 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
113 114 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
121 122 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
122 123 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
123 124 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
124 125 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
125 126 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
126 127 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
127 128 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
128 129 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
129 130 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
130 131 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
131 132 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
232 241 9.853177 CTGGAATTCAAGGGAATAATTACTAGT 57.147 33.333 7.93 0.00 42.87 2.57
415 424 3.803021 GCTCTCTGCTAATCATGTCAGGG 60.803 52.174 0.00 0.00 38.95 4.45
438 447 2.935201 GGCTCATGAGTGAAGCACTAAG 59.065 50.000 23.38 0.00 45.44 2.18
579 588 3.612251 GCAGCCAGCCATGTCAAT 58.388 55.556 0.00 0.00 37.23 2.57
598 607 4.737177 AAGGGAGCAGCAGCCAGC 62.737 66.667 0.00 0.00 43.56 4.85
688 697 3.133691 TGGTAATCATCAAGATGCTCGC 58.866 45.455 5.19 0.00 38.65 5.03
713 722 2.498644 TAATTGATGGCCACGTCCAA 57.501 45.000 8.16 10.93 39.96 3.53
805 814 2.557805 CGCGCCATGGATATGCAC 59.442 61.111 18.40 0.00 32.79 4.57
806 815 2.557805 GCGCCATGGATATGCACG 59.442 61.111 18.40 8.73 36.22 5.34
807 816 2.253758 GCGCCATGGATATGCACGT 61.254 57.895 18.40 0.00 35.82 4.49
808 817 0.948623 GCGCCATGGATATGCACGTA 60.949 55.000 18.40 0.00 35.82 3.57
809 818 0.790207 CGCCATGGATATGCACGTAC 59.210 55.000 18.40 0.00 32.79 3.67
893 902 9.609346 ACTACTCCATGTTACAATAATTGTACC 57.391 33.333 0.00 0.00 45.16 3.34
1016 1025 0.745845 CAATCAAGCAGGCGGTAGCT 60.746 55.000 0.00 0.00 44.31 3.32
1311 1341 0.325671 AGGGACCTGGACATGATCGT 60.326 55.000 0.00 0.00 0.00 3.73
1330 1360 1.771255 GTGGAGGACATGGGAAGCTAT 59.229 52.381 0.00 0.00 0.00 2.97
1352 1382 0.808453 GTACGGCGCCTGATTAGCAA 60.808 55.000 26.68 0.00 0.00 3.91
1392 1426 3.303990 GGTGTGTACGTACGAGTTCTTCA 60.304 47.826 24.41 8.46 0.00 3.02
1393 1427 3.904824 GTGTGTACGTACGAGTTCTTCAG 59.095 47.826 24.41 0.00 0.00 3.02
1412 1446 0.107831 GTGGCTGTTGGGTAGTGTCA 59.892 55.000 0.00 0.00 0.00 3.58
1420 1455 3.962063 TGTTGGGTAGTGTCAGTTCTGTA 59.038 43.478 0.00 0.00 0.00 2.74
1432 1467 0.939419 GTTCTGTACGCCGTTTGGTT 59.061 50.000 0.00 0.00 37.67 3.67
1435 1470 0.658897 CTGTACGCCGTTTGGTTGTT 59.341 50.000 0.00 0.00 37.67 2.83
1455 1490 4.683781 TGTTTTGTTCTGTGCTGTGTTTTC 59.316 37.500 0.00 0.00 0.00 2.29
1456 1491 4.511617 TTTGTTCTGTGCTGTGTTTTCA 57.488 36.364 0.00 0.00 0.00 2.69
1481 1516 1.481871 TCCCCGAATGTGTACTCCTC 58.518 55.000 0.00 0.00 0.00 3.71
1490 1530 5.488341 GAATGTGTACTCCTCCTTTGCTTA 58.512 41.667 0.00 0.00 0.00 3.09
1519 1559 3.619038 CAGAGTAAAGAAATCCCGCTGTC 59.381 47.826 0.00 0.00 0.00 3.51
1520 1560 3.515901 AGAGTAAAGAAATCCCGCTGTCT 59.484 43.478 0.00 0.00 0.00 3.41
1521 1561 3.600388 AGTAAAGAAATCCCGCTGTCTG 58.400 45.455 0.00 0.00 0.00 3.51
1522 1562 2.568623 AAAGAAATCCCGCTGTCTGT 57.431 45.000 0.00 0.00 0.00 3.41
1523 1563 2.568623 AAGAAATCCCGCTGTCTGTT 57.431 45.000 0.00 0.00 0.00 3.16
1524 1564 2.568623 AGAAATCCCGCTGTCTGTTT 57.431 45.000 0.00 0.00 0.00 2.83
1541 1581 6.090628 TGTCTGTTTCAAATTTGCAGTGTTTC 59.909 34.615 13.54 1.90 0.00 2.78
1547 1587 2.514205 ATTTGCAGTGTTTCTGGCAC 57.486 45.000 0.00 0.00 43.78 5.01
1570 1610 7.302524 CACAGGTAAAAATTTACATACGTGCT 58.697 34.615 20.07 11.59 43.64 4.40
1583 1623 6.461110 ACATACGTGCTTAGGTTACAGTAT 57.539 37.500 0.00 0.00 0.00 2.12
1584 1624 7.572523 ACATACGTGCTTAGGTTACAGTATA 57.427 36.000 0.00 0.00 0.00 1.47
1585 1625 7.999679 ACATACGTGCTTAGGTTACAGTATAA 58.000 34.615 0.00 0.00 0.00 0.98
1586 1626 8.636213 ACATACGTGCTTAGGTTACAGTATAAT 58.364 33.333 0.00 0.00 0.00 1.28
1588 1628 5.751990 ACGTGCTTAGGTTACAGTATAATGC 59.248 40.000 0.00 0.00 0.00 3.56
1589 1629 5.107989 CGTGCTTAGGTTACAGTATAATGCG 60.108 44.000 0.00 0.00 0.00 4.73
1592 1632 5.981315 GCTTAGGTTACAGTATAATGCGACA 59.019 40.000 0.00 0.00 0.00 4.35
1593 1633 6.144080 GCTTAGGTTACAGTATAATGCGACAG 59.856 42.308 0.00 0.00 0.00 3.51
1613 1653 1.683917 GAGCTCTTCGGAAGCAGGATA 59.316 52.381 12.90 0.00 0.00 2.59
1649 1690 8.421249 TTTTCATTCCAAAGGATGATACAGTT 57.579 30.769 0.00 0.00 0.00 3.16
1650 1691 7.395190 TTCATTCCAAAGGATGATACAGTTG 57.605 36.000 0.00 0.00 0.00 3.16
1654 1701 6.367374 TCCAAAGGATGATACAGTTGTGTA 57.633 37.500 0.00 0.00 43.43 2.90
1693 1740 0.671251 CTAAGCCGAGAGCCGAGAAT 59.329 55.000 0.00 0.00 45.47 2.40
1709 1756 3.165124 GAGAATCGTCGCTAATCCGATC 58.835 50.000 0.00 0.00 40.17 3.69
1724 1771 1.374343 CGATCCCAGACGGAGAACGA 61.374 60.000 0.00 0.00 46.60 3.85
1734 1781 1.080093 GGAGAACGACGATGCCACA 60.080 57.895 0.00 0.00 0.00 4.17
1867 1914 2.593725 CGAGGCGGATCCGGTAGA 60.594 66.667 33.98 0.00 40.77 2.59
1884 1936 3.773370 ACGACCTGTCACCGTGAT 58.227 55.556 4.13 0.00 35.02 3.06
1885 1937 2.046938 ACGACCTGTCACCGTGATT 58.953 52.632 4.13 0.00 35.02 2.57
1886 1938 0.391597 ACGACCTGTCACCGTGATTT 59.608 50.000 4.13 0.00 35.02 2.17
1887 1939 1.202604 ACGACCTGTCACCGTGATTTT 60.203 47.619 4.13 0.00 35.02 1.82
1888 1940 1.871039 CGACCTGTCACCGTGATTTTT 59.129 47.619 4.13 0.00 0.00 1.94
1943 1995 0.389025 TATCGTGCGCATGACCTCAT 59.611 50.000 33.17 19.78 36.96 2.90
1955 2007 4.473520 CCTCATCCGGCCGTGCTT 62.474 66.667 26.12 2.04 0.00 3.91
1956 2008 2.436646 CTCATCCGGCCGTGCTTT 60.437 61.111 26.12 0.00 0.00 3.51
1958 2010 1.586154 CTCATCCGGCCGTGCTTTTT 61.586 55.000 26.12 0.00 0.00 1.94
1960 2012 1.901464 ATCCGGCCGTGCTTTTTGT 60.901 52.632 26.12 0.00 0.00 2.83
1961 2013 1.460273 ATCCGGCCGTGCTTTTTGTT 61.460 50.000 26.12 0.00 0.00 2.83
1962 2014 1.227118 CCGGCCGTGCTTTTTGTTT 60.227 52.632 26.12 0.00 0.00 2.83
1963 2015 1.486644 CCGGCCGTGCTTTTTGTTTG 61.487 55.000 26.12 0.00 0.00 2.93
1964 2016 0.804156 CGGCCGTGCTTTTTGTTTGT 60.804 50.000 19.50 0.00 0.00 2.83
1965 2017 0.649993 GGCCGTGCTTTTTGTTTGTG 59.350 50.000 0.00 0.00 0.00 3.33
1966 2018 0.026156 GCCGTGCTTTTTGTTTGTGC 59.974 50.000 0.00 0.00 0.00 4.57
1967 2019 1.639280 CCGTGCTTTTTGTTTGTGCT 58.361 45.000 0.00 0.00 0.00 4.40
1968 2020 1.324134 CCGTGCTTTTTGTTTGTGCTG 59.676 47.619 0.00 0.00 0.00 4.41
1969 2021 1.266989 CGTGCTTTTTGTTTGTGCTGC 60.267 47.619 0.00 0.00 0.00 5.25
1970 2022 2.001872 GTGCTTTTTGTTTGTGCTGCT 58.998 42.857 0.00 0.00 0.00 4.24
1971 2023 2.029606 GTGCTTTTTGTTTGTGCTGCTC 59.970 45.455 0.00 0.00 0.00 4.26
1972 2024 1.256117 GCTTTTTGTTTGTGCTGCTCG 59.744 47.619 0.00 0.00 0.00 5.03
1973 2025 2.796304 CTTTTTGTTTGTGCTGCTCGA 58.204 42.857 0.00 0.00 0.00 4.04
1974 2026 2.929531 TTTTGTTTGTGCTGCTCGAA 57.070 40.000 0.00 0.06 0.00 3.71
1975 2027 3.435105 TTTTGTTTGTGCTGCTCGAAT 57.565 38.095 7.56 0.00 0.00 3.34
1976 2028 2.686558 TTGTTTGTGCTGCTCGAATC 57.313 45.000 7.56 3.44 0.00 2.52
2201 2282 6.919662 TGCTCATGATTTCAAAGAAAGTTCAC 59.080 34.615 0.00 0.00 0.00 3.18
2220 2301 5.506686 TCACGGATTCAAAAATGTTGACA 57.493 34.783 0.00 0.00 0.00 3.58
2223 2304 6.813649 TCACGGATTCAAAAATGTTGACAAAA 59.186 30.769 0.00 0.00 0.00 2.44
2225 2306 8.759641 CACGGATTCAAAAATGTTGACAAAATA 58.240 29.630 0.00 0.00 0.00 1.40
2294 2384 9.226606 AGGATTTGAAATAGTGTTCACGAATTA 57.773 29.630 0.00 0.00 37.24 1.40
2404 2495 9.829507 ATGTTTGTGGATTTGAAAAATGTTAGA 57.170 25.926 0.00 0.00 0.00 2.10
2405 2496 9.658799 TGTTTGTGGATTTGAAAAATGTTAGAA 57.341 25.926 0.00 0.00 0.00 2.10
2468 2563 9.829507 TTTGAAAATTGATTGTGAATACCAAGT 57.170 25.926 0.00 0.00 0.00 3.16
2480 2576 4.327898 TGAATACCAAGTTGTTCGCGTATC 59.672 41.667 5.77 0.00 0.00 2.24
2506 2602 9.362539 CTACAAAAATGATCAAGGATTTGGAAG 57.637 33.333 20.38 15.69 34.97 3.46
2510 2606 9.850198 AAAAATGATCAAGGATTTGGAAGAAAA 57.150 25.926 0.00 0.00 34.97 2.29
2513 2609 8.605325 ATGATCAAGGATTTGGAAGAAAATCT 57.395 30.769 0.00 0.00 43.25 2.40
2514 2610 8.059798 TGATCAAGGATTTGGAAGAAAATCTC 57.940 34.615 0.00 1.14 43.25 2.75
2515 2611 6.840780 TCAAGGATTTGGAAGAAAATCTCC 57.159 37.500 8.96 0.00 43.25 3.71
2516 2612 6.314120 TCAAGGATTTGGAAGAAAATCTCCA 58.686 36.000 8.96 0.00 43.25 3.86
2517 2613 6.955851 TCAAGGATTTGGAAGAAAATCTCCAT 59.044 34.615 8.96 0.00 43.25 3.41
2518 2614 8.115384 TCAAGGATTTGGAAGAAAATCTCCATA 58.885 33.333 8.96 0.00 43.25 2.74
2520 2616 8.899887 AGGATTTGGAAGAAAATCTCCATAAA 57.100 30.769 8.96 0.00 43.25 1.40
2521 2617 9.498039 AGGATTTGGAAGAAAATCTCCATAAAT 57.502 29.630 8.96 0.00 43.25 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.967380 TTCGGACGGAGGGAGTAACC 60.967 60.000 0.00 0.00 38.08 2.85
5 6 0.890683 TTTCGGACGGAGGGAGTAAC 59.109 55.000 0.00 0.00 0.00 2.50
6 7 1.631405 TTTTCGGACGGAGGGAGTAA 58.369 50.000 0.00 0.00 0.00 2.24
7 8 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
8 9 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
9 10 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
10 11 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
11 12 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
12 13 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
13 14 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
14 15 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
15 16 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
16 17 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
17 18 9.490663 CTATTTTGATGACAAGTATTTTCGGAC 57.509 33.333 0.00 0.00 37.32 4.79
18 19 9.443323 TCTATTTTGATGACAAGTATTTTCGGA 57.557 29.630 0.00 0.00 37.32 4.55
73 74 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
79 80 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
82 83 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
83 84 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
84 85 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
85 86 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
86 87 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
87 88 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
95 96 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
96 97 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
97 98 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
98 99 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
99 100 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
100 101 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
101 102 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
102 103 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
103 104 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
104 105 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
105 106 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
106 107 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
107 108 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
108 109 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
109 110 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
110 111 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
111 112 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
112 113 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
113 114 5.603170 ATTACTTCCTCCGTCCGAAAATA 57.397 39.130 0.00 0.00 0.00 1.40
114 115 3.967332 TTACTTCCTCCGTCCGAAAAT 57.033 42.857 0.00 0.00 0.00 1.82
115 116 3.967332 ATTACTTCCTCCGTCCGAAAA 57.033 42.857 0.00 0.00 0.00 2.29
116 117 3.967332 AATTACTTCCTCCGTCCGAAA 57.033 42.857 0.00 0.00 0.00 3.46
117 118 4.220382 TGTTAATTACTTCCTCCGTCCGAA 59.780 41.667 0.00 0.00 0.00 4.30
118 119 3.763360 TGTTAATTACTTCCTCCGTCCGA 59.237 43.478 0.00 0.00 0.00 4.55
119 120 4.114058 TGTTAATTACTTCCTCCGTCCG 57.886 45.455 0.00 0.00 0.00 4.79
120 121 4.331992 GCTTGTTAATTACTTCCTCCGTCC 59.668 45.833 0.00 0.00 0.00 4.79
121 122 4.933400 TGCTTGTTAATTACTTCCTCCGTC 59.067 41.667 0.00 0.00 0.00 4.79
122 123 4.694037 GTGCTTGTTAATTACTTCCTCCGT 59.306 41.667 0.00 0.00 0.00 4.69
123 124 4.935808 AGTGCTTGTTAATTACTTCCTCCG 59.064 41.667 0.00 0.00 0.00 4.63
124 125 6.819397 AAGTGCTTGTTAATTACTTCCTCC 57.181 37.500 0.00 0.00 0.00 4.30
232 241 5.308014 TGCTAACGGTTCTATACGGAGATA 58.692 41.667 0.00 0.00 0.00 1.98
415 424 1.742880 TGCTTCACTCATGAGCCGC 60.743 57.895 22.83 18.28 35.83 6.53
494 503 4.177165 TCCTACGAGCGTAAACAAATGA 57.823 40.909 4.20 0.00 0.00 2.57
579 588 3.251509 TGGCTGCTGCTCCCTTGA 61.252 61.111 15.64 0.00 39.59 3.02
598 607 1.865865 AGTCAACTTGGCACGTACTG 58.134 50.000 0.00 0.00 0.00 2.74
615 624 6.314896 GTGCTCTCATCTTTGCAAAGTATAGT 59.685 38.462 32.46 15.54 37.17 2.12
688 697 2.099592 ACGTGGCCATCAATTAAGCATG 59.900 45.455 9.72 0.00 0.00 4.06
713 722 3.477530 GTCTGGTTAAGGACTTGCTTGT 58.522 45.455 0.00 0.00 0.00 3.16
805 814 1.591248 GCATTGACTTTGTGCGTACG 58.409 50.000 11.84 11.84 0.00 3.67
806 815 1.401018 GGGCATTGACTTTGTGCGTAC 60.401 52.381 0.00 0.00 39.69 3.67
807 816 0.878416 GGGCATTGACTTTGTGCGTA 59.122 50.000 0.00 0.00 39.69 4.42
808 817 0.823356 AGGGCATTGACTTTGTGCGT 60.823 50.000 0.00 0.00 39.69 5.24
809 818 0.314935 AAGGGCATTGACTTTGTGCG 59.685 50.000 0.00 0.00 39.69 5.34
893 902 2.987149 CTGTTCACCAGTACTAACAGCG 59.013 50.000 18.57 3.27 41.49 5.18
989 998 3.429085 CGCCTGCTTGATTGAATTACAC 58.571 45.455 0.00 0.00 0.00 2.90
1016 1025 5.466058 GCTCTAGCTACTACTACGATGTGAA 59.534 44.000 0.00 0.00 38.21 3.18
1129 1156 3.573772 CTCCGGCAGCGAGAACACA 62.574 63.158 0.00 0.00 0.00 3.72
1264 1294 3.585990 GCCATCGACATTGCCCGG 61.586 66.667 0.00 0.00 0.00 5.73
1311 1341 2.196742 ATAGCTTCCCATGTCCTCCA 57.803 50.000 0.00 0.00 0.00 3.86
1330 1360 1.269413 GCTAATCAGGCGCCGTACTTA 60.269 52.381 23.20 15.85 0.00 2.24
1392 1426 0.396811 GACACTACCCAACAGCCACT 59.603 55.000 0.00 0.00 0.00 4.00
1393 1427 0.107831 TGACACTACCCAACAGCCAC 59.892 55.000 0.00 0.00 0.00 5.01
1412 1446 0.105408 ACCAAACGGCGTACAGAACT 59.895 50.000 15.20 0.00 0.00 3.01
1420 1455 0.244178 ACAAAACAACCAAACGGCGT 59.756 45.000 6.77 6.77 0.00 5.68
1432 1467 3.932545 AACACAGCACAGAACAAAACA 57.067 38.095 0.00 0.00 0.00 2.83
1435 1470 4.022416 AGTGAAAACACAGCACAGAACAAA 60.022 37.500 0.00 0.00 35.08 2.83
1455 1490 1.604604 ACACATTCGGGGAAACAGTG 58.395 50.000 0.00 0.00 32.92 3.66
1456 1491 2.370849 AGTACACATTCGGGGAAACAGT 59.629 45.455 0.00 0.00 0.00 3.55
1457 1492 3.000727 GAGTACACATTCGGGGAAACAG 58.999 50.000 0.00 0.00 0.00 3.16
1460 1495 2.235402 GAGGAGTACACATTCGGGGAAA 59.765 50.000 0.00 0.00 0.00 3.13
1464 1499 1.486211 AGGAGGAGTACACATTCGGG 58.514 55.000 0.00 0.00 0.00 5.14
1466 1501 2.673368 GCAAAGGAGGAGTACACATTCG 59.327 50.000 0.00 0.00 0.00 3.34
1481 1516 2.039084 ACTCTGGTCAGGTAAGCAAAGG 59.961 50.000 0.00 0.00 0.00 3.11
1490 1530 4.019231 GGGATTTCTTTACTCTGGTCAGGT 60.019 45.833 0.00 0.00 0.00 4.00
1519 1559 6.455913 CCAGAAACACTGCAAATTTGAAACAG 60.456 38.462 22.31 19.51 44.52 3.16
1520 1560 5.350914 CCAGAAACACTGCAAATTTGAAACA 59.649 36.000 22.31 9.32 44.52 2.83
1521 1561 5.727515 GCCAGAAACACTGCAAATTTGAAAC 60.728 40.000 22.31 4.90 44.52 2.78
1522 1562 4.332268 GCCAGAAACACTGCAAATTTGAAA 59.668 37.500 22.31 7.99 44.52 2.69
1523 1563 3.870419 GCCAGAAACACTGCAAATTTGAA 59.130 39.130 22.31 10.82 44.52 2.69
1524 1564 3.118847 TGCCAGAAACACTGCAAATTTGA 60.119 39.130 22.31 6.29 44.52 2.69
1541 1581 6.745450 CGTATGTAAATTTTTACCTGTGCCAG 59.255 38.462 9.96 0.00 41.72 4.85
1547 1587 9.485591 CTAAGCACGTATGTAAATTTTTACCTG 57.514 33.333 9.96 0.00 41.72 4.00
1570 1610 7.337480 TCTGTCGCATTATACTGTAACCTAA 57.663 36.000 0.00 0.00 0.00 2.69
1583 1623 1.202302 CCGAAGAGCTCTGTCGCATTA 60.202 52.381 28.09 0.00 33.46 1.90
1584 1624 0.459237 CCGAAGAGCTCTGTCGCATT 60.459 55.000 28.09 11.10 33.46 3.56
1585 1625 1.140589 CCGAAGAGCTCTGTCGCAT 59.859 57.895 28.09 11.73 33.46 4.73
1586 1626 1.524008 TTCCGAAGAGCTCTGTCGCA 61.524 55.000 28.09 19.10 33.46 5.10
1588 1628 0.800300 GCTTCCGAAGAGCTCTGTCG 60.800 60.000 27.23 27.23 37.18 4.35
1589 1629 0.244994 TGCTTCCGAAGAGCTCTGTC 59.755 55.000 19.06 15.23 40.75 3.51
1592 1632 0.613292 TCCTGCTTCCGAAGAGCTCT 60.613 55.000 11.45 11.45 40.75 4.09
1593 1633 0.463620 ATCCTGCTTCCGAAGAGCTC 59.536 55.000 12.54 5.27 40.75 4.09
1632 1672 8.777413 CATATACACAACTGTATCATCCTTTGG 58.223 37.037 0.00 0.00 41.83 3.28
1649 1690 4.539726 ACGGTAGGAGTTCCATATACACA 58.460 43.478 0.28 0.00 38.89 3.72
1650 1691 4.320057 CGACGGTAGGAGTTCCATATACAC 60.320 50.000 0.28 0.00 38.89 2.90
1654 1701 1.612463 GCGACGGTAGGAGTTCCATAT 59.388 52.381 0.28 0.00 38.89 1.78
1693 1740 0.820482 TGGGATCGGATTAGCGACGA 60.820 55.000 0.00 0.00 41.20 4.20
1709 1756 1.654954 ATCGTCGTTCTCCGTCTGGG 61.655 60.000 0.00 0.00 37.94 4.45
1724 1771 2.669569 GCACCACTGTGGCATCGT 60.670 61.111 26.20 3.75 42.67 3.73
1763 1810 1.003331 CTGCTACCATCGACTCGTCTC 60.003 57.143 0.00 0.00 0.00 3.36
1855 1902 3.028969 GGTCGTCTACCGGATCCG 58.971 66.667 27.65 27.65 38.88 4.18
1867 1914 0.391597 AAATCACGGTGACAGGTCGT 59.608 50.000 13.92 0.00 37.64 4.34
1889 1941 5.066634 TGTGCCGATGTCAGTTTCTTAAAAA 59.933 36.000 0.00 0.00 0.00 1.94
1890 1942 4.576873 TGTGCCGATGTCAGTTTCTTAAAA 59.423 37.500 0.00 0.00 0.00 1.52
1891 1943 4.130857 TGTGCCGATGTCAGTTTCTTAAA 58.869 39.130 0.00 0.00 0.00 1.52
1892 1944 3.734463 TGTGCCGATGTCAGTTTCTTAA 58.266 40.909 0.00 0.00 0.00 1.85
1894 1946 2.146342 CTGTGCCGATGTCAGTTTCTT 58.854 47.619 0.00 0.00 0.00 2.52
1900 1952 3.857854 GCGCTGTGCCGATGTCAG 61.858 66.667 0.00 0.00 37.76 3.51
1943 1995 1.668101 AAACAAAAAGCACGGCCGGA 61.668 50.000 31.76 0.00 0.00 5.14
1955 2007 2.929531 TTCGAGCAGCACAAACAAAA 57.070 40.000 0.00 0.00 0.00 2.44
1956 2008 2.287547 GGATTCGAGCAGCACAAACAAA 60.288 45.455 0.00 0.00 0.00 2.83
1958 2010 0.874390 GGATTCGAGCAGCACAAACA 59.126 50.000 0.00 0.00 0.00 2.83
1960 2012 0.960364 GGGGATTCGAGCAGCACAAA 60.960 55.000 0.00 0.00 0.00 2.83
1961 2013 1.377202 GGGGATTCGAGCAGCACAA 60.377 57.895 0.00 0.00 0.00 3.33
1962 2014 2.268920 GGGGATTCGAGCAGCACA 59.731 61.111 0.00 0.00 0.00 4.57
1963 2015 2.514824 GGGGGATTCGAGCAGCAC 60.515 66.667 0.00 0.00 0.00 4.40
1964 2016 2.329539 GATGGGGGATTCGAGCAGCA 62.330 60.000 0.00 0.00 0.00 4.41
1965 2017 1.599240 GATGGGGGATTCGAGCAGC 60.599 63.158 0.00 0.00 0.00 5.25
1966 2018 1.301244 CGATGGGGGATTCGAGCAG 60.301 63.158 0.00 0.00 37.55 4.24
1967 2019 2.821685 CGATGGGGGATTCGAGCA 59.178 61.111 0.00 0.00 37.55 4.26
1968 2020 2.666526 GCGATGGGGGATTCGAGC 60.667 66.667 0.00 0.00 37.55 5.03
1969 2021 2.356313 CGCGATGGGGGATTCGAG 60.356 66.667 0.00 0.00 37.55 4.04
1970 2022 4.602259 GCGCGATGGGGGATTCGA 62.602 66.667 12.10 0.00 37.55 3.71
2165 2219 2.916702 TCATGAGCACTGTGTGAACT 57.083 45.000 9.86 0.00 35.23 3.01
2173 2227 6.444633 ACTTTCTTTGAAATCATGAGCACTG 58.555 36.000 0.09 0.00 0.00 3.66
2220 2301 6.255887 TGACGCCACGAACAAATTTTTATTTT 59.744 30.769 0.00 0.00 0.00 1.82
2223 2304 4.861210 TGACGCCACGAACAAATTTTTAT 58.139 34.783 0.00 0.00 0.00 1.40
2225 2306 3.152261 TGACGCCACGAACAAATTTTT 57.848 38.095 0.00 0.00 0.00 1.94
2462 2557 2.450609 AGATACGCGAACAACTTGGT 57.549 45.000 15.93 0.00 0.00 3.67
2467 2562 6.301108 TCATTTTTGTAGATACGCGAACAAC 58.699 36.000 15.93 4.69 31.92 3.32
2468 2563 6.469139 TCATTTTTGTAGATACGCGAACAA 57.531 33.333 15.93 11.98 0.00 2.83
2480 2576 9.362539 CTTCCAAATCCTTGATCATTTTTGTAG 57.637 33.333 0.00 2.02 34.14 2.74


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

AutoCloner maintained by Alex Coulton.