Multiple sequence alignment - TraesCS5B01G129900

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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 TraesCS5B01G129900 chr5B 100.000 2610 0 0 1 2610 241169083 241171692 0.000000e+00 4820.0
1 TraesCS5B01G129900 chr5B 96.226 53 1 1 328 379 241169332 241169384 4.630000e-13 86.1
2 TraesCS5B01G129900 chr5B 96.226 53 1 1 250 302 241169410 241169461 4.630000e-13 86.1
3 TraesCS5B01G129900 chr5A 88.900 2027 98 48 1 1958 291595883 291597851 0.000000e+00 2379.0
4 TraesCS5B01G129900 chr5A 91.420 338 18 2 871 1208 556716977 556716651 1.100000e-123 453.0
5 TraesCS5B01G129900 chr5A 85.677 384 34 14 1955 2327 291598079 291598452 4.070000e-103 385.0
6 TraesCS5B01G129900 chr5A 89.956 229 18 4 2384 2608 664887368 664887141 9.140000e-75 291.0
7 TraesCS5B01G129900 chr5A 89.565 230 19 4 2383 2608 496333171 496332943 1.180000e-73 287.0
8 TraesCS5B01G129900 chr5A 89.520 229 19 4 2384 2608 666134498 666134725 4.250000e-73 285.0
9 TraesCS5B01G129900 chr5A 90.506 158 13 2 1369 1525 556716552 556716396 9.470000e-50 207.0
10 TraesCS5B01G129900 chr5A 91.667 120 10 0 1003 1122 291600638 291600757 1.610000e-37 167.0
11 TraesCS5B01G129900 chr5D 91.130 1646 61 31 1 1625 218560266 218561847 0.000000e+00 2152.0
12 TraesCS5B01G129900 chr5D 88.342 935 68 21 1682 2608 218562003 218562904 0.000000e+00 1085.0
13 TraesCS5B01G129900 chr5D 90.164 122 12 0 1003 1124 218564694 218564815 2.690000e-35 159.0
14 TraesCS5B01G129900 chr5D 96.226 53 1 1 250 302 218560590 218560641 4.630000e-13 86.1
15 TraesCS5B01G129900 chr5D 94.340 53 2 1 328 379 218560512 218560564 2.150000e-11 80.5
16 TraesCS5B01G129900 chr2A 91.066 347 20 2 862 1208 703274106 703274441 2.370000e-125 459.0
17 TraesCS5B01G129900 chr2A 89.873 158 14 2 1369 1525 703274540 703274696 4.400000e-48 202.0
18 TraesCS5B01G129900 chr7A 90.490 347 22 2 862 1208 450885569 450885904 5.120000e-122 448.0
19 TraesCS5B01G129900 chr7A 90.746 335 19 4 862 1196 660580574 660580896 1.110000e-118 436.0
20 TraesCS5B01G129900 chr7A 89.130 230 20 4 2383 2608 653010765 653010537 5.500000e-72 281.0
21 TraesCS5B01G129900 chr7A 87.917 240 23 5 2370 2604 37122456 37122694 7.110000e-71 278.0
22 TraesCS5B01G129900 chr7A 92.105 152 11 1 1369 1520 450886003 450886153 2.030000e-51 213.0
23 TraesCS5B01G129900 chr3A 89.625 347 25 3 862 1208 211756019 211756354 5.160000e-117 431.0
24 TraesCS5B01G129900 chr3A 90.000 230 18 4 2383 2608 80080950 80080722 2.540000e-75 292.0
25 TraesCS5B01G129900 chr6D 87.243 243 27 3 2370 2608 422201740 422201982 9.200000e-70 274.0
26 TraesCS5B01G129900 chr4D 87.395 238 25 4 2375 2608 350270075 350269839 4.280000e-68 268.0
27 TraesCS5B01G129900 chr1D 87.342 237 26 3 2376 2608 7401934 7401698 4.280000e-68 268.0


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 TraesCS5B01G129900 chr5B 241169083 241171692 2609 False 1664.066667 4820 97.4840 1 2610 3 chr5B.!!$F1 2609
1 TraesCS5B01G129900 chr5A 291595883 291600757 4874 False 977.000000 2379 88.7480 1 2327 3 chr5A.!!$F2 2326
2 TraesCS5B01G129900 chr5A 556716396 556716977 581 True 330.000000 453 90.9630 871 1525 2 chr5A.!!$R3 654
3 TraesCS5B01G129900 chr5D 218560266 218564815 4549 False 712.520000 2152 92.0404 1 2608 5 chr5D.!!$F1 2607
4 TraesCS5B01G129900 chr2A 703274106 703274696 590 False 330.500000 459 90.4695 862 1525 2 chr2A.!!$F1 663
5 TraesCS5B01G129900 chr7A 450885569 450886153 584 False 330.500000 448 91.2975 862 1520 2 chr7A.!!$F3 658

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
706 723 0.036483 CACACATCCATGTCGGTCCA 60.036 55.0 0.0 0.0 39.39 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2423 0.037046 CCAGGGGCAGCAATTGAAAC 60.037 55.0 10.34 0.0 0.0 2.78 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
284 290 7.809331 TGACTGTTTTAATGCAGATGAATGAAC 59.191 33.333 12.06 0.00 36.62 3.18
447 453 3.641434 AGCATCAAGATTAGCTGGTGT 57.359 42.857 0.00 0.00 35.72 4.16
448 454 3.539604 AGCATCAAGATTAGCTGGTGTC 58.460 45.455 0.00 0.00 35.72 3.67
449 455 2.615912 GCATCAAGATTAGCTGGTGTCC 59.384 50.000 0.00 0.00 0.00 4.02
465 471 0.321653 GTCCTCCTGTTTGCATCCGT 60.322 55.000 0.00 0.00 0.00 4.69
501 507 1.070601 TGCTGCTTGCTTCAGTGTCTA 59.929 47.619 0.00 0.00 43.37 2.59
650 661 8.078060 TCACAACATCTAACTCCAGAATGATA 57.922 34.615 0.00 0.00 39.69 2.15
706 723 0.036483 CACACATCCATGTCGGTCCA 60.036 55.000 0.00 0.00 39.39 4.02
713 730 2.203938 ATGTCGGTCCAGTGGGGT 60.204 61.111 9.92 0.00 38.11 4.95
740 757 4.152647 TCATGGCTCGTGGTAGATCTAAT 58.847 43.478 3.40 0.00 0.00 1.73
750 769 6.320418 TCGTGGTAGATCTAATAGTGCTCAAA 59.680 38.462 3.40 0.00 0.00 2.69
761 780 1.406539 AGTGCTCAAAACCAACAGCAG 59.593 47.619 0.00 0.00 42.47 4.24
762 781 0.746063 TGCTCAAAACCAACAGCAGG 59.254 50.000 0.00 0.00 36.96 4.85
764 783 0.675633 CTCAAAACCAACAGCAGGGG 59.324 55.000 0.00 0.00 0.00 4.79
765 784 0.758685 TCAAAACCAACAGCAGGGGG 60.759 55.000 0.00 0.00 0.00 5.40
796 823 3.728845 ACAACTACAAGTGTACTGCCAG 58.271 45.455 0.00 0.00 0.00 4.85
804 831 1.625818 AGTGTACTGCCAGGAAGAAGG 59.374 52.381 0.00 0.00 0.00 3.46
808 835 2.575805 ACTGCCAGGAAGAAGGAAAG 57.424 50.000 0.00 0.00 0.00 2.62
840 871 2.732412 ACAGTGAGTGATTCCTGTCG 57.268 50.000 0.00 0.00 34.33 4.35
902 933 1.302383 CGTCCATAAAACGGCCAGCA 61.302 55.000 2.24 0.00 36.51 4.41
979 1011 0.752743 TGGCTCAGCTTTGCACTTGT 60.753 50.000 0.00 0.00 0.00 3.16
980 1012 0.318445 GGCTCAGCTTTGCACTTGTG 60.318 55.000 0.00 0.00 0.00 3.33
981 1013 0.664761 GCTCAGCTTTGCACTTGTGA 59.335 50.000 4.79 0.00 0.00 3.58
982 1014 1.598924 GCTCAGCTTTGCACTTGTGAC 60.599 52.381 4.79 0.00 0.00 3.67
983 1015 1.945394 CTCAGCTTTGCACTTGTGACT 59.055 47.619 4.79 0.00 0.00 3.41
984 1016 2.357009 CTCAGCTTTGCACTTGTGACTT 59.643 45.455 4.79 0.00 0.00 3.01
985 1017 2.097954 TCAGCTTTGCACTTGTGACTTG 59.902 45.455 4.79 0.00 0.00 3.16
1110 1142 2.223377 GCTCGACACCGTCAAATTCTTT 59.777 45.455 0.00 0.00 37.05 2.52
1121 1153 2.554893 TCAAATTCTTTGGGTGGTACGC 59.445 45.455 0.19 0.00 40.98 4.42
1180 1216 3.366374 GGATTCCAACTTTACTGCACAGC 60.366 47.826 0.00 0.00 0.00 4.40
1199 1235 0.307760 CACACTTCAAACTGTCCGCC 59.692 55.000 0.00 0.00 0.00 6.13
1263 1304 8.833231 TGACCAAAACTATCTCAAAGTCTAAG 57.167 34.615 0.00 0.00 0.00 2.18
1275 1316 3.838244 AAGTCTAAGTCAGCAACACCA 57.162 42.857 0.00 0.00 0.00 4.17
1276 1317 3.393089 AGTCTAAGTCAGCAACACCAG 57.607 47.619 0.00 0.00 0.00 4.00
1278 1319 3.580458 AGTCTAAGTCAGCAACACCAGAT 59.420 43.478 0.00 0.00 0.00 2.90
1357 1398 4.400884 TCTGACAAGACAAGAGATAGGAGC 59.599 45.833 0.00 0.00 0.00 4.70
1367 1408 6.171921 ACAAGAGATAGGAGCATATCATTGC 58.828 40.000 14.48 0.00 43.09 3.56
1513 1554 1.739562 CCACGAGAAGCACTCTGCC 60.740 63.158 8.78 0.00 46.52 4.85
1617 1658 0.394565 GAGGCCGCCTGAATGATACT 59.605 55.000 19.21 0.00 31.76 2.12
1625 1666 2.412591 CCTGAATGATACTCCCCACCT 58.587 52.381 0.00 0.00 0.00 4.00
1626 1667 2.105477 CCTGAATGATACTCCCCACCTG 59.895 54.545 0.00 0.00 0.00 4.00
1627 1668 2.774234 CTGAATGATACTCCCCACCTGT 59.226 50.000 0.00 0.00 0.00 4.00
1630 1671 1.866015 TGATACTCCCCACCTGTCTG 58.134 55.000 0.00 0.00 0.00 3.51
1659 1776 2.802816 GCAAGTAAGCATCTACCATCGG 59.197 50.000 0.00 0.00 0.00 4.18
1723 1863 3.844211 TGTGATGTACCTAAAGCCTCCTT 59.156 43.478 0.00 0.00 0.00 3.36
1724 1864 4.288626 TGTGATGTACCTAAAGCCTCCTTT 59.711 41.667 0.00 0.00 43.43 3.11
1725 1865 5.222048 TGTGATGTACCTAAAGCCTCCTTTT 60.222 40.000 0.00 0.00 41.37 2.27
1758 1900 0.108945 GTCCTGCTACTACGGCGTTT 60.109 55.000 21.24 8.65 0.00 3.60
1759 1901 0.108992 TCCTGCTACTACGGCGTTTG 60.109 55.000 21.24 14.60 0.00 2.93
1760 1902 0.389426 CCTGCTACTACGGCGTTTGT 60.389 55.000 21.24 19.80 0.00 2.83
1761 1903 1.425412 CTGCTACTACGGCGTTTGTT 58.575 50.000 21.24 2.43 0.00 2.83
1762 1904 2.598589 CTGCTACTACGGCGTTTGTTA 58.401 47.619 21.24 0.00 0.00 2.41
1763 1905 2.988493 CTGCTACTACGGCGTTTGTTAA 59.012 45.455 21.24 0.00 0.00 2.01
1783 1925 0.824759 CCGTCTAGCCTGTAAAGCCT 59.175 55.000 0.00 0.00 0.00 4.58
1785 1927 1.202428 CGTCTAGCCTGTAAAGCCTCC 60.202 57.143 0.00 0.00 0.00 4.30
1787 1929 0.105039 CTAGCCTGTAAAGCCTCCGG 59.895 60.000 0.00 0.00 0.00 5.14
1814 1956 4.868171 GTGTAACTCTATTCCGTGCATTCA 59.132 41.667 0.00 0.00 0.00 2.57
1910 2060 9.458727 GATGAATTGATGGATATCTGTAATGGT 57.541 33.333 2.05 0.00 34.31 3.55
1917 2067 6.806668 TGGATATCTGTAATGGTTCACTCA 57.193 37.500 2.05 0.00 0.00 3.41
1922 2072 4.910195 TCTGTAATGGTTCACTCATGCTT 58.090 39.130 0.00 0.00 0.00 3.91
1934 2084 1.746787 CTCATGCTTGCCACTATTGCA 59.253 47.619 0.00 0.00 38.05 4.08
1958 2341 4.836125 AACACTAAACTCTGGCAATGTG 57.164 40.909 0.00 0.00 0.00 3.21
1967 2350 3.755378 ACTCTGGCAATGTGAGTTTCATC 59.245 43.478 1.61 0.00 37.76 2.92
1989 2372 4.097437 TCAATGAAGCTGAAGGCATTGATC 59.903 41.667 17.67 0.00 46.71 2.92
2019 2402 8.509690 AGTAACATGTCAGAATTTTCATGTGAG 58.490 33.333 0.00 0.00 46.33 3.51
2026 2409 4.868171 CAGAATTTTCATGTGAGGGCATTG 59.132 41.667 0.00 0.00 0.00 2.82
2028 2411 5.424252 AGAATTTTCATGTGAGGGCATTGAT 59.576 36.000 0.00 0.00 0.00 2.57
2030 2413 6.795144 ATTTTCATGTGAGGGCATTGATAA 57.205 33.333 0.00 0.00 0.00 1.75
2031 2414 6.602410 TTTTCATGTGAGGGCATTGATAAA 57.398 33.333 0.00 0.00 0.00 1.40
2032 2415 5.581126 TTCATGTGAGGGCATTGATAAAC 57.419 39.130 0.00 0.00 0.00 2.01
2033 2416 4.598022 TCATGTGAGGGCATTGATAAACA 58.402 39.130 0.00 0.00 0.00 2.83
2034 2417 5.202765 TCATGTGAGGGCATTGATAAACAT 58.797 37.500 0.00 0.00 0.00 2.71
2035 2418 5.657745 TCATGTGAGGGCATTGATAAACATT 59.342 36.000 0.00 0.00 0.00 2.71
2037 2420 4.160065 TGTGAGGGCATTGATAAACATTGG 59.840 41.667 0.00 0.00 32.52 3.16
2038 2421 3.132646 TGAGGGCATTGATAAACATTGGC 59.867 43.478 0.00 0.00 46.96 4.52
2040 2423 2.472816 GGCATTGATAAACATTGGCCG 58.527 47.619 0.00 0.00 44.19 6.13
2088 2471 0.026803 GCGGTGCTATCTTTCTTGCG 59.973 55.000 0.00 0.00 0.00 4.85
2141 2525 1.079681 CCCATGCACACAACCATGC 60.080 57.895 0.00 0.00 42.40 4.06
2162 2554 7.255242 CCATGCCATCTTGTTAATAGTCGAAAT 60.255 37.037 0.00 0.00 0.00 2.17
2165 2557 7.126398 GCCATCTTGTTAATAGTCGAAATGTC 58.874 38.462 0.00 0.00 0.00 3.06
2208 2601 7.915293 TGTCAAATGGTAATACTGTCGAATT 57.085 32.000 0.00 0.00 0.00 2.17
2219 2612 9.355215 GTAATACTGTCGAATTGAAAGAAGAGA 57.645 33.333 0.00 0.00 35.30 3.10
2222 2615 4.956085 TGTCGAATTGAAAGAAGAGACCA 58.044 39.130 0.00 0.00 0.00 4.02
2232 2625 5.466728 TGAAAGAAGAGACCAAAAGTGATCG 59.533 40.000 0.00 0.00 0.00 3.69
2237 2630 1.279271 AGACCAAAAGTGATCGAGGGG 59.721 52.381 0.00 0.00 0.00 4.79
2238 2631 0.322546 ACCAAAAGTGATCGAGGGGC 60.323 55.000 0.00 0.00 0.00 5.80
2239 2632 0.035056 CCAAAAGTGATCGAGGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
2240 2633 1.373570 CAAAAGTGATCGAGGGGCTC 58.626 55.000 0.00 0.00 0.00 4.70
2241 2634 0.253327 AAAAGTGATCGAGGGGCTCC 59.747 55.000 0.00 0.00 0.00 4.70
2249 2642 1.801242 TCGAGGGGCTCCATGAAATA 58.199 50.000 4.79 0.00 34.83 1.40
2284 2678 6.096846 CCTTGGGAAAAAGATGGACGATAAAT 59.903 38.462 0.00 0.00 0.00 1.40
2353 4078 0.538977 AATGGAAGCTGCACTGCACT 60.539 50.000 0.00 0.03 33.79 4.40
2354 4079 1.241990 ATGGAAGCTGCACTGCACTG 61.242 55.000 0.00 0.00 33.79 3.66
2355 4080 2.254651 GAAGCTGCACTGCACTGC 59.745 61.111 10.99 10.99 37.70 4.40
2356 4081 2.517638 AAGCTGCACTGCACTGCA 60.518 55.556 18.27 18.27 45.06 4.41
2357 4082 2.728427 GAAGCTGCACTGCACTGCAC 62.728 60.000 15.89 12.79 42.36 4.57
2360 4085 1.890510 CTGCACTGCACTGCACAGA 60.891 57.895 15.89 0.00 42.36 3.41
2406 4131 7.486407 TCTAACCGATCCCTTAAAAGTTAGT 57.514 36.000 0.00 0.00 37.51 2.24
2408 4133 5.750352 ACCGATCCCTTAAAAGTTAGTGA 57.250 39.130 0.00 0.00 0.00 3.41
2409 4134 5.485620 ACCGATCCCTTAAAAGTTAGTGAC 58.514 41.667 0.00 0.00 0.00 3.67
2410 4135 5.247792 ACCGATCCCTTAAAAGTTAGTGACT 59.752 40.000 0.00 0.00 41.47 3.41
2411 4136 6.438425 ACCGATCCCTTAAAAGTTAGTGACTA 59.562 38.462 0.00 0.00 37.72 2.59
2413 4138 7.277319 CCGATCCCTTAAAAGTTAGTGACTAAC 59.723 40.741 24.09 24.09 44.52 2.34
2414 4139 7.277319 CGATCCCTTAAAAGTTAGTGACTAACC 59.723 40.741 26.80 12.68 45.08 2.85
2415 4140 7.622502 TCCCTTAAAAGTTAGTGACTAACCT 57.377 36.000 26.80 15.18 45.08 3.50
2417 4142 7.290714 TCCCTTAAAAGTTAGTGACTAACCTCA 59.709 37.037 26.80 11.04 45.08 3.86
2418 4143 7.603024 CCCTTAAAAGTTAGTGACTAACCTCAG 59.397 40.741 26.80 16.91 45.08 3.35
2419 4144 8.148999 CCTTAAAAGTTAGTGACTAACCTCAGT 58.851 37.037 26.80 13.50 45.08 3.41
2420 4145 8.882415 TTAAAAGTTAGTGACTAACCTCAGTG 57.118 34.615 26.80 0.00 45.08 3.66
2421 4146 5.470047 AAGTTAGTGACTAACCTCAGTGG 57.530 43.478 26.80 0.00 45.08 4.00
2423 4148 4.767928 AGTTAGTGACTAACCTCAGTGGAG 59.232 45.833 26.80 0.00 45.08 3.86
2425 4150 4.383931 AGTGACTAACCTCAGTGGAGTA 57.616 45.455 0.00 0.00 39.64 2.59
2426 4151 4.936802 AGTGACTAACCTCAGTGGAGTAT 58.063 43.478 0.00 0.00 39.64 2.12
2427 4152 6.075949 AGTGACTAACCTCAGTGGAGTATA 57.924 41.667 0.00 0.00 39.64 1.47
2428 4153 6.674573 AGTGACTAACCTCAGTGGAGTATAT 58.325 40.000 0.00 0.00 39.64 0.86
2429 4154 7.813331 AGTGACTAACCTCAGTGGAGTATATA 58.187 38.462 0.00 0.00 39.64 0.86
2430 4155 8.449625 AGTGACTAACCTCAGTGGAGTATATAT 58.550 37.037 0.00 0.00 39.64 0.86
2431 4156 9.736414 GTGACTAACCTCAGTGGAGTATATATA 57.264 37.037 0.00 0.00 39.64 0.86
2432 4157 9.736414 TGACTAACCTCAGTGGAGTATATATAC 57.264 37.037 14.05 14.05 39.64 1.47
2433 4158 9.962809 GACTAACCTCAGTGGAGTATATATACT 57.037 37.037 22.67 22.67 45.73 2.12
2461 4186 1.201414 GATTTTGCCACACCTAACCGG 59.799 52.381 0.00 0.00 39.35 5.28
2465 4190 2.263540 CCACACCTAACCGGTCCG 59.736 66.667 8.04 3.60 44.93 4.79
2523 4248 8.430063 CAAATTCAATCAGATTTGAACCGAAAG 58.570 33.333 9.06 0.00 45.55 2.62
2552 4277 9.190858 GATGCATTTAAACATAAGTTCAACACA 57.809 29.630 0.00 0.00 36.84 3.72
2563 4288 9.561069 ACATAAGTTCAACACATAAAGTTCTCT 57.439 29.630 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 8.350722 TCTAATCTATAACAGACATCCGTTCAC 58.649 37.037 0.00 0.00 35.62 3.18
284 290 4.334759 CCATCCTGTTTGTTAGCTCATCAG 59.665 45.833 0.00 0.00 0.00 2.90
447 453 0.400213 AACGGATGCAAACAGGAGGA 59.600 50.000 0.00 0.00 0.00 3.71
448 454 1.068333 CAAACGGATGCAAACAGGAGG 60.068 52.381 0.00 0.00 0.00 4.30
449 455 1.068333 CCAAACGGATGCAAACAGGAG 60.068 52.381 0.00 0.00 0.00 3.69
465 471 2.244000 GCACGCTGCTACTTCCAAA 58.756 52.632 0.00 0.00 40.96 3.28
488 494 3.641436 TGGAGAAACTAGACACTGAAGCA 59.359 43.478 0.00 0.00 0.00 3.91
693 710 2.290287 CCCACTGGACCGACATGGA 61.290 63.158 0.00 0.00 42.00 3.41
695 712 2.268920 CCCCACTGGACCGACATG 59.731 66.667 0.00 0.00 35.39 3.21
740 757 2.618241 CTGCTGTTGGTTTTGAGCACTA 59.382 45.455 0.00 0.00 36.54 2.74
762 781 2.026636 TGTAGTTGTAGACAATGCCCCC 60.027 50.000 0.00 0.00 38.24 5.40
764 783 4.154195 CACTTGTAGTTGTAGACAATGCCC 59.846 45.833 0.00 0.00 38.24 5.36
765 784 4.755123 ACACTTGTAGTTGTAGACAATGCC 59.245 41.667 0.00 0.00 38.24 4.40
796 823 9.058174 GTAAATAGCCTTATCTTTCCTTCTTCC 57.942 37.037 0.00 0.00 0.00 3.46
804 831 8.821894 CACTCACTGTAAATAGCCTTATCTTTC 58.178 37.037 0.00 0.00 0.00 2.62
808 835 8.894768 AATCACTCACTGTAAATAGCCTTATC 57.105 34.615 0.00 0.00 0.00 1.75
902 933 0.880278 GCGTATCATCATGCCACGGT 60.880 55.000 11.40 0.00 33.39 4.83
979 1011 2.288666 GGCTCAACAAGTCACAAGTCA 58.711 47.619 0.00 0.00 0.00 3.41
980 1012 2.288666 TGGCTCAACAAGTCACAAGTC 58.711 47.619 0.00 0.00 33.69 3.01
981 1013 2.418368 TGGCTCAACAAGTCACAAGT 57.582 45.000 0.00 0.00 33.69 3.16
982 1014 2.030540 CCATGGCTCAACAAGTCACAAG 60.031 50.000 0.00 0.00 43.89 3.16
983 1015 1.955778 CCATGGCTCAACAAGTCACAA 59.044 47.619 0.00 0.00 43.89 3.33
984 1016 1.142667 TCCATGGCTCAACAAGTCACA 59.857 47.619 6.96 0.00 43.89 3.58
985 1017 1.808945 CTCCATGGCTCAACAAGTCAC 59.191 52.381 6.96 0.00 43.89 3.67
1110 1142 0.610509 AAATGCATGCGTACCACCCA 60.611 50.000 13.96 0.00 0.00 4.51
1180 1216 0.307760 GGCGGACAGTTTGAAGTGTG 59.692 55.000 8.82 0.00 42.36 3.82
1263 1304 2.771089 TCTTCATCTGGTGTTGCTGAC 58.229 47.619 0.00 0.00 0.00 3.51
1275 1316 6.164876 CGATGCCTAATCTTGATCTTCATCT 58.835 40.000 0.00 0.00 32.61 2.90
1276 1317 5.163874 GCGATGCCTAATCTTGATCTTCATC 60.164 44.000 0.00 0.00 32.61 2.92
1278 1319 4.060900 GCGATGCCTAATCTTGATCTTCA 58.939 43.478 0.00 0.00 32.61 3.02
1367 1408 3.243839 CCCCAACACAAGGAACAATCAAG 60.244 47.826 0.00 0.00 0.00 3.02
1513 1554 2.436646 ATGAAGGTGGCGGCGAAG 60.437 61.111 12.98 0.00 0.00 3.79
1617 1658 3.170717 CTTAGTAACAGACAGGTGGGGA 58.829 50.000 0.00 0.00 0.00 4.81
1625 1666 5.849510 TGCTTACTTGCTTAGTAACAGACA 58.150 37.500 7.61 3.34 42.89 3.41
1626 1667 6.814146 AGATGCTTACTTGCTTAGTAACAGAC 59.186 38.462 7.61 8.96 42.89 3.51
1627 1668 6.936279 AGATGCTTACTTGCTTAGTAACAGA 58.064 36.000 7.61 0.00 42.89 3.41
1630 1671 7.039882 TGGTAGATGCTTACTTGCTTAGTAAC 58.960 38.462 7.61 6.49 42.89 2.50
1659 1776 3.267974 GCACCTTACAGTGGCTGC 58.732 61.111 0.00 0.00 38.24 5.25
1758 1900 4.813027 CTTTACAGGCTAGACGGTTAACA 58.187 43.478 6.71 0.00 0.00 2.41
1759 1901 3.615937 GCTTTACAGGCTAGACGGTTAAC 59.384 47.826 6.71 0.00 0.00 2.01
1760 1902 3.368739 GGCTTTACAGGCTAGACGGTTAA 60.369 47.826 6.71 3.14 42.53 2.01
1761 1903 2.167075 GGCTTTACAGGCTAGACGGTTA 59.833 50.000 6.71 0.00 42.53 2.85
1762 1904 1.066358 GGCTTTACAGGCTAGACGGTT 60.066 52.381 6.71 0.00 42.53 4.44
1763 1905 0.535797 GGCTTTACAGGCTAGACGGT 59.464 55.000 6.61 6.61 42.53 4.83
1785 1927 1.537562 GGAATAGAGTTACACCGGCCG 60.538 57.143 21.04 21.04 0.00 6.13
1787 1929 1.135721 ACGGAATAGAGTTACACCGGC 59.864 52.381 0.00 0.00 43.76 6.13
1788 1930 2.805845 CACGGAATAGAGTTACACCGG 58.194 52.381 0.00 0.00 43.76 5.28
1789 1931 2.190981 GCACGGAATAGAGTTACACCG 58.809 52.381 0.00 0.00 44.77 4.94
1814 1956 6.273071 GTGATAACCAAGCAACTTTTGAACT 58.727 36.000 0.00 0.00 0.00 3.01
1910 2060 2.857186 TAGTGGCAAGCATGAGTGAA 57.143 45.000 0.00 0.00 0.00 3.18
1917 2067 4.160065 TGTTTATGCAATAGTGGCAAGCAT 59.840 37.500 14.11 14.11 45.60 3.79
1922 2072 6.432783 AGTTTAGTGTTTATGCAATAGTGGCA 59.567 34.615 0.00 0.00 46.66 4.92
1934 2084 6.714810 TCACATTGCCAGAGTTTAGTGTTTAT 59.285 34.615 0.00 0.00 0.00 1.40
1958 2341 5.638783 CCTTCAGCTTCATTGATGAAACTC 58.361 41.667 6.65 1.17 45.26 3.01
1967 2350 3.861276 TCAATGCCTTCAGCTTCATTG 57.139 42.857 12.48 12.48 44.12 2.82
1989 2372 8.908678 CATGAAAATTCTGACATGTTACTGTTG 58.091 33.333 0.00 0.00 36.42 3.33
2019 2402 2.802774 CGGCCAATGTTTATCAATGCCC 60.803 50.000 2.24 0.00 35.82 5.36
2026 2409 5.445806 GCAATTGAAACGGCCAATGTTTATC 60.446 40.000 10.34 0.00 39.51 1.75
2028 2411 3.743396 GCAATTGAAACGGCCAATGTTTA 59.257 39.130 10.34 0.00 39.51 2.01
2030 2413 2.142319 GCAATTGAAACGGCCAATGTT 58.858 42.857 10.34 0.00 34.75 2.71
2031 2414 1.344114 AGCAATTGAAACGGCCAATGT 59.656 42.857 10.34 0.00 34.75 2.71
2032 2415 1.727880 CAGCAATTGAAACGGCCAATG 59.272 47.619 10.34 0.00 34.75 2.82
2033 2416 1.940752 GCAGCAATTGAAACGGCCAAT 60.941 47.619 10.34 0.00 35.92 3.16
2034 2417 0.599728 GCAGCAATTGAAACGGCCAA 60.600 50.000 10.34 0.00 0.00 4.52
2035 2418 1.006337 GCAGCAATTGAAACGGCCA 60.006 52.632 10.34 0.00 0.00 5.36
2037 2420 1.737735 GGGCAGCAATTGAAACGGC 60.738 57.895 10.34 3.88 0.00 5.68
2038 2421 1.079888 GGGGCAGCAATTGAAACGG 60.080 57.895 10.34 0.00 0.00 4.44
2039 2422 0.388907 CAGGGGCAGCAATTGAAACG 60.389 55.000 10.34 0.00 0.00 3.60
2040 2423 0.037046 CCAGGGGCAGCAATTGAAAC 60.037 55.000 10.34 0.00 0.00 2.78
2088 2471 9.396022 TCATTCTTGGTAATAATGAAGGAGAAC 57.604 33.333 0.00 0.00 36.85 3.01
2125 2509 0.248012 ATGGCATGGTTGTGTGCATG 59.752 50.000 0.00 0.00 43.00 4.06
2141 2525 8.331022 CAGACATTTCGACTATTAACAAGATGG 58.669 37.037 0.00 0.00 0.00 3.51
2165 2557 3.733337 ACAAAGTCTGCAGTAACTCCAG 58.267 45.455 14.67 6.90 0.00 3.86
2208 2601 5.466728 CGATCACTTTTGGTCTCTTCTTTCA 59.533 40.000 0.00 0.00 29.58 2.69
2219 2612 0.322546 GCCCCTCGATCACTTTTGGT 60.323 55.000 0.00 0.00 0.00 3.67
2222 2615 0.253327 GGAGCCCCTCGATCACTTTT 59.747 55.000 0.00 0.00 0.00 2.27
2232 2625 3.648545 ACTAGTATTTCATGGAGCCCCTC 59.351 47.826 0.00 0.00 0.00 4.30
2237 2630 7.631717 AGGAAAAACTAGTATTTCATGGAGC 57.368 36.000 0.00 0.00 37.29 4.70
2238 2631 8.462016 CCAAGGAAAAACTAGTATTTCATGGAG 58.538 37.037 14.45 0.00 41.61 3.86
2239 2632 7.396055 CCCAAGGAAAAACTAGTATTTCATGGA 59.604 37.037 18.65 0.00 41.61 3.41
2240 2633 7.396055 TCCCAAGGAAAAACTAGTATTTCATGG 59.604 37.037 13.33 13.33 40.30 3.66
2241 2634 8.348285 TCCCAAGGAAAAACTAGTATTTCATG 57.652 34.615 0.00 0.00 37.29 3.07
2274 2667 2.375146 AGCAAACCCCATTTATCGTCC 58.625 47.619 0.00 0.00 0.00 4.79
2319 4037 5.945784 AGCTTCCATTGTTGCAGTTATCTTA 59.054 36.000 0.00 0.00 0.00 2.10
2320 4038 4.768968 AGCTTCCATTGTTGCAGTTATCTT 59.231 37.500 0.00 0.00 0.00 2.40
2355 4080 4.201950 GCCCTAAGCACATACAAATCTGTG 60.202 45.833 0.00 0.00 44.40 3.66
2356 4081 3.947834 GCCCTAAGCACATACAAATCTGT 59.052 43.478 0.00 0.00 42.97 3.41
2357 4082 4.558538 GCCCTAAGCACATACAAATCTG 57.441 45.455 0.00 0.00 42.97 2.90
2388 4113 7.277319 GGTTAGTCACTAACTTTTAAGGGATCG 59.723 40.741 23.94 0.00 43.89 3.69
2406 4131 9.736414 GTATATATACTCCACTGAGGTTAGTCA 57.264 37.037 14.53 0.00 43.29 3.41
2423 4148 9.819267 GGCAAAATCCTAGTGGAGTATATATAC 57.181 37.037 14.05 14.05 46.91 1.47
2425 4150 8.322091 GTGGCAAAATCCTAGTGGAGTATATAT 58.678 37.037 0.00 0.00 46.91 0.86
2426 4151 7.291416 TGTGGCAAAATCCTAGTGGAGTATATA 59.709 37.037 0.00 0.00 46.91 0.86
2427 4152 6.101150 TGTGGCAAAATCCTAGTGGAGTATAT 59.899 38.462 0.00 0.00 46.91 0.86
2428 4153 5.427157 TGTGGCAAAATCCTAGTGGAGTATA 59.573 40.000 0.00 0.00 46.91 1.47
2429 4154 4.227300 TGTGGCAAAATCCTAGTGGAGTAT 59.773 41.667 0.00 0.00 46.91 2.12
2430 4155 3.585289 TGTGGCAAAATCCTAGTGGAGTA 59.415 43.478 0.00 0.00 46.91 2.59
2431 4156 2.375174 TGTGGCAAAATCCTAGTGGAGT 59.625 45.455 0.00 0.00 46.91 3.85
2432 4157 2.749621 GTGTGGCAAAATCCTAGTGGAG 59.250 50.000 0.00 0.00 46.91 3.86
2434 4159 1.818674 GGTGTGGCAAAATCCTAGTGG 59.181 52.381 0.00 0.00 0.00 4.00
2435 4160 2.795329 AGGTGTGGCAAAATCCTAGTG 58.205 47.619 0.00 0.00 0.00 2.74
2436 4161 4.332828 GTTAGGTGTGGCAAAATCCTAGT 58.667 43.478 0.00 0.00 33.23 2.57
2437 4162 3.694566 GGTTAGGTGTGGCAAAATCCTAG 59.305 47.826 0.00 0.00 33.23 3.02
2438 4163 3.692690 GGTTAGGTGTGGCAAAATCCTA 58.307 45.455 0.00 0.00 0.00 2.94
2439 4164 2.525368 GGTTAGGTGTGGCAAAATCCT 58.475 47.619 0.00 0.00 0.00 3.24
2440 4165 1.201414 CGGTTAGGTGTGGCAAAATCC 59.799 52.381 0.00 0.00 0.00 3.01
2441 4166 1.201414 CCGGTTAGGTGTGGCAAAATC 59.799 52.381 0.00 0.00 34.51 2.17
2442 4167 1.253100 CCGGTTAGGTGTGGCAAAAT 58.747 50.000 0.00 0.00 34.51 1.82
2443 4168 2.721945 CCGGTTAGGTGTGGCAAAA 58.278 52.632 0.00 0.00 34.51 2.44
2444 4169 4.484987 CCGGTTAGGTGTGGCAAA 57.515 55.556 0.00 0.00 34.51 3.68
2476 4201 9.567848 AATTTGTGCAAATTTAGTTATACTCCG 57.432 29.630 14.88 0.00 45.67 4.63
2509 4234 4.985413 TGCATCATCTTTCGGTTCAAATC 58.015 39.130 0.00 0.00 0.00 2.17
2552 4277 8.842358 TTAATGTTCGGTTGAGAGAACTTTAT 57.158 30.769 13.51 0.00 44.95 1.40


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

AutoCloner maintained by Alex Coulton.