Multiple sequence alignment - TraesCS4D01G133100

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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 TraesCS4D01G133100 chr4D 100.000 3043 0 0 1 3043 119807307 119804265 0.000000e+00 5620.0
1 TraesCS4D01G133100 chr4D 96.450 169 4 2 2249 2416 119805020 119804853 8.310000e-71 278.0
2 TraesCS4D01G133100 chr4D 96.450 169 4 2 2288 2455 119805059 119804892 8.310000e-71 278.0
3 TraesCS4D01G133100 chr4D 96.124 129 4 1 2249 2376 119804981 119804853 3.070000e-50 209.0
4 TraesCS4D01G133100 chr4D 96.124 129 4 1 2327 2455 119805059 119804932 3.070000e-50 209.0
5 TraesCS4D01G133100 chr4D 98.851 87 0 1 2252 2337 119804939 119804853 1.460000e-33 154.0
6 TraesCS4D01G133100 chr4D 98.851 87 0 1 2369 2455 119805056 119804971 1.460000e-33 154.0
7 TraesCS4D01G133100 chr4D 100.000 50 0 0 2249 2298 119804902 119804853 3.230000e-15 93.5
8 TraesCS4D01G133100 chr4D 100.000 50 0 0 2406 2455 119805059 119805010 3.230000e-15 93.5
9 TraesCS4D01G133100 chr4A 91.251 1543 78 29 787 2298 450765826 450764310 0.000000e+00 2049.0
10 TraesCS4D01G133100 chr4A 91.727 689 37 4 1 680 450766592 450765915 0.000000e+00 939.0
11 TraesCS4D01G133100 chr4A 87.832 641 29 5 2406 3043 450764359 450763765 0.000000e+00 706.0
12 TraesCS4D01G133100 chr4A 91.429 70 6 0 1451 1520 667005050 667005119 2.500000e-16 97.1
13 TraesCS4D01G133100 chr4B 91.140 1456 56 30 869 2298 182261146 182259738 0.000000e+00 1906.0
14 TraesCS4D01G133100 chr4B 93.855 716 25 6 1 699 182270743 182270030 0.000000e+00 1061.0
15 TraesCS4D01G133100 chr4B 94.053 639 29 2 2406 3043 182259787 182259157 0.000000e+00 961.0
16 TraesCS4D01G133100 chr4B 95.402 87 4 0 802 888 182261254 182261168 4.090000e-29 139.0
17 TraesCS4D01G133100 chr5A 78.131 535 91 22 1035 1560 337941135 337941652 1.760000e-82 316.0
18 TraesCS4D01G133100 chr5A 80.100 201 40 0 1797 1997 337942992 337943192 1.890000e-32 150.0
19 TraesCS4D01G133100 chr5B 78.067 538 90 24 1035 1566 288178287 288177772 6.330000e-82 315.0
20 TraesCS4D01G133100 chr5B 79.048 210 44 0 1797 2006 288176431 288176222 8.790000e-31 145.0
21 TraesCS4D01G133100 chr5D 83.951 324 49 3 1245 1566 254586679 254587001 1.060000e-79 307.0
22 TraesCS4D01G133100 chr5D 79.104 201 42 0 1797 1997 254588340 254588540 4.090000e-29 139.0
23 TraesCS4D01G133100 chr3A 93.056 72 5 0 1449 1520 625330514 625330585 4.150000e-19 106.0
24 TraesCS4D01G133100 chr7A 95.000 60 3 0 1449 1508 602227128 602227187 8.980000e-16 95.3
25 TraesCS4D01G133100 chr2B 90.278 72 6 1 1449 1520 699179954 699180024 3.230000e-15 93.5
26 TraesCS4D01G133100 chr2A 78.151 119 21 3 1449 1563 176671130 176671247 1.510000e-08 71.3


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 TraesCS4D01G133100 chr4D 119804265 119807307 3042 True 787.666667 5620 98.094444 1 3043 9 chr4D.!!$R1 3042
1 TraesCS4D01G133100 chr4A 450763765 450766592 2827 True 1231.333333 2049 90.270000 1 3043 3 chr4A.!!$R1 3042
2 TraesCS4D01G133100 chr4B 182270030 182270743 713 True 1061.000000 1061 93.855000 1 699 1 chr4B.!!$R1 698
3 TraesCS4D01G133100 chr4B 182259157 182261254 2097 True 1002.000000 1906 93.531667 802 3043 3 chr4B.!!$R2 2241
4 TraesCS4D01G133100 chr5A 337941135 337943192 2057 False 233.000000 316 79.115500 1035 1997 2 chr5A.!!$F1 962
5 TraesCS4D01G133100 chr5B 288176222 288178287 2065 True 230.000000 315 78.557500 1035 2006 2 chr5B.!!$R1 971
6 TraesCS4D01G133100 chr5D 254586679 254588540 1861 False 223.000000 307 81.527500 1245 1997 2 chr5D.!!$F1 752

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
785 812 0.109039 TGAATGTCGGTCGCGATGAA 60.109 50.0 14.06 5.49 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 3940 0.025001 CCTTCATTTGCGACGTAGCG 59.975 55.0 15.98 4.09 40.67 4.26 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
27 28 1.668101 GGAGAGGGGTAGCGACACAG 61.668 65.000 0.44 0.00 0.00 3.66
104 105 2.511452 CCCTGCATACCCTCCTCCG 61.511 68.421 0.00 0.00 0.00 4.63
182 183 2.148611 TGGCTATCCATCAGCAGGG 58.851 57.895 0.00 0.00 40.95 4.45
194 195 4.519437 GCAGGGGCGTACGGGTAC 62.519 72.222 18.39 0.00 0.00 3.34
304 322 2.094286 GGCTACTCGATCCATGGATCTG 60.094 54.545 39.11 33.24 46.36 2.90
315 333 2.791655 CATGGATCTGTCATGGATGGG 58.208 52.381 0.00 0.00 38.55 4.00
321 339 0.830648 CTGTCATGGATGGGTACGGT 59.169 55.000 0.00 0.00 0.00 4.83
468 486 1.202806 CCTGCGGGTTACCATCATCAT 60.203 52.381 2.29 0.00 36.13 2.45
510 528 0.249741 ATGGACGCTACGGTTATGGC 60.250 55.000 0.00 0.00 0.00 4.40
623 650 4.938080 TCTTCCAAGTTGATCTATCGAGC 58.062 43.478 3.87 0.00 0.00 5.03
699 726 5.549228 TCCATCCATATCCCATATCCATAGC 59.451 44.000 0.00 0.00 0.00 2.97
700 727 5.311385 CCATCCATATCCCATATCCATAGCA 59.689 44.000 0.00 0.00 0.00 3.49
701 728 6.011893 CCATCCATATCCCATATCCATAGCAT 60.012 42.308 0.00 0.00 0.00 3.79
702 729 7.183293 CCATCCATATCCCATATCCATAGCATA 59.817 40.741 0.00 0.00 0.00 3.14
703 730 8.779031 CATCCATATCCCATATCCATAGCATAT 58.221 37.037 0.00 0.00 0.00 1.78
745 772 1.882682 TAAGTTCGTTCTGTGCGCGC 61.883 55.000 27.26 27.26 0.00 6.86
755 782 2.911280 GTGCGCGCACGTATAGTC 59.089 61.111 43.80 22.52 42.83 2.59
756 783 1.585521 GTGCGCGCACGTATAGTCT 60.586 57.895 43.80 0.00 42.83 3.24
757 784 0.316442 GTGCGCGCACGTATAGTCTA 60.316 55.000 43.80 12.23 42.83 2.59
758 785 0.316442 TGCGCGCACGTATAGTCTAC 60.316 55.000 33.09 0.00 42.83 2.59
759 786 1.319010 GCGCGCACGTATAGTCTACG 61.319 60.000 29.10 6.54 45.44 3.51
771 798 7.762241 CGTATAGTCTACGTACATGTGAATG 57.238 40.000 9.11 0.00 36.31 2.67
777 804 2.602878 ACGTACATGTGAATGTCGGTC 58.397 47.619 9.11 0.00 36.08 4.79
783 810 1.075979 TGTGAATGTCGGTCGCGATG 61.076 55.000 14.06 8.75 0.00 3.84
784 811 0.800683 GTGAATGTCGGTCGCGATGA 60.801 55.000 14.06 11.38 0.00 2.92
785 812 0.109039 TGAATGTCGGTCGCGATGAA 60.109 50.000 14.06 5.49 0.00 2.57
846 898 1.024579 GCAATCCACACCCTGTACGG 61.025 60.000 0.00 0.00 0.00 4.02
859 911 2.223433 CCTGTACGGTCGATCTGTAACC 60.223 54.545 0.00 0.00 39.29 2.85
888 940 4.630940 CCAATTTAAACATGCACCCACATC 59.369 41.667 0.00 0.00 0.00 3.06
890 942 6.350864 CCAATTTAAACATGCACCCACATCTA 60.351 38.462 0.00 0.00 0.00 1.98
891 943 7.267128 CAATTTAAACATGCACCCACATCTAT 58.733 34.615 0.00 0.00 0.00 1.98
893 945 3.939740 AACATGCACCCACATCTATCT 57.060 42.857 0.00 0.00 0.00 1.98
894 946 5.372343 AAACATGCACCCACATCTATCTA 57.628 39.130 0.00 0.00 0.00 1.98
895 947 5.573380 AACATGCACCCACATCTATCTAT 57.427 39.130 0.00 0.00 0.00 1.98
922 1018 1.651987 AATACGAACGTGCTCCCATG 58.348 50.000 10.14 0.00 0.00 3.66
957 1054 7.025963 GCTTTCAGACAATTTCGATCTTGATT 58.974 34.615 12.80 0.60 0.00 2.57
964 1065 8.669243 AGACAATTTCGATCTTGATTAGTTTCC 58.331 33.333 12.80 0.00 0.00 3.13
1029 1144 1.369689 CAGCAGCAGCAACGTTGAC 60.370 57.895 31.62 21.18 45.49 3.18
1062 1177 5.681982 CGAGTACGAGGAAGAATACATCAAC 59.318 44.000 0.00 0.00 42.66 3.18
1171 1286 7.312888 GGTACGTACTACAATAATTGCTACG 57.687 40.000 24.07 0.00 37.62 3.51
1185 1300 6.604735 AATTGCTACGTACCTTCATCAATC 57.395 37.500 0.00 0.00 0.00 2.67
1193 1308 2.898705 ACCTTCATCAATCGAGCTGAC 58.101 47.619 0.00 0.00 0.00 3.51
1198 1313 4.397481 TCATCAATCGAGCTGACTGATT 57.603 40.909 7.18 2.06 40.50 2.57
1229 1345 3.670627 GCTAGCACCATTACAAGCAACAC 60.671 47.826 10.63 0.00 0.00 3.32
1237 1357 6.748658 CACCATTACAAGCAACACTATTGATG 59.251 38.462 0.00 0.00 0.00 3.07
1916 3217 1.142097 GACGCTCAAGCTCTACCCC 59.858 63.158 0.00 0.00 39.32 4.95
1974 3275 3.574396 AGAGAACATCGACAAGGTCTTCA 59.426 43.478 3.74 0.00 0.00 3.02
2049 3356 3.371063 GGGACGACTGACGCCTCA 61.371 66.667 0.00 0.00 46.94 3.86
2150 3462 8.438676 AATTATCAATTACTGTACACTCCAGC 57.561 34.615 0.00 0.00 33.09 4.85
2220 3543 6.178239 ACGTGGAATGAGTTAATTTACTGC 57.822 37.500 1.04 0.00 0.00 4.40
2243 3566 3.604582 ACTCTAGTTTCTCAGCATTGCC 58.395 45.455 4.70 0.00 0.00 4.52
2245 3568 2.573462 TCTAGTTTCTCAGCATTGCCCT 59.427 45.455 4.70 0.00 0.00 5.19
2247 3570 0.813821 GTTTCTCAGCATTGCCCTCC 59.186 55.000 4.70 0.00 0.00 4.30
2248 3571 0.405198 TTTCTCAGCATTGCCCTCCA 59.595 50.000 4.70 0.00 0.00 3.86
2250 3573 1.001764 CTCAGCATTGCCCTCCACA 60.002 57.895 4.70 0.00 0.00 4.17
2251 3574 1.001764 TCAGCATTGCCCTCCACAG 60.002 57.895 4.70 0.00 0.00 3.66
2252 3575 2.362120 AGCATTGCCCTCCACAGC 60.362 61.111 4.70 0.00 0.00 4.40
2253 3576 3.455469 GCATTGCCCTCCACAGCC 61.455 66.667 0.00 0.00 0.00 4.85
2254 3577 2.357836 CATTGCCCTCCACAGCCT 59.642 61.111 0.00 0.00 0.00 4.58
2255 3578 1.751927 CATTGCCCTCCACAGCCTC 60.752 63.158 0.00 0.00 0.00 4.70
2256 3579 2.988839 ATTGCCCTCCACAGCCTCC 61.989 63.158 0.00 0.00 0.00 4.30
2273 3596 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
2274 3597 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
2275 3598 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
2276 3599 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
2277 3600 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
2278 3601 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
2286 3609 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
2288 3611 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
2289 3612 2.027192 GTGGAGATCACCAAAGGCTACA 60.027 50.000 13.92 0.00 41.87 2.74
2290 3613 2.237143 TGGAGATCACCAAAGGCTACAG 59.763 50.000 9.69 0.00 36.96 2.74
2291 3614 2.284190 GAGATCACCAAAGGCTACAGC 58.716 52.381 0.00 0.00 41.14 4.40
2312 3635 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
2313 3636 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
2314 3637 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
2315 3638 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
2316 3639 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
2317 3640 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
2325 3648 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
2342 3665 1.908483 CTACAGCCTCCCCACTTCC 59.092 63.158 0.00 0.00 0.00 3.46
2366 3689 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
2367 3690 1.207089 TGGAGATCACCAAAGGCTACG 59.793 52.381 9.69 0.00 36.96 3.51
2368 3691 1.473434 GGAGATCACCAAAGGCTACGG 60.473 57.143 4.05 0.72 0.00 4.02
2369 3692 0.107654 AGATCACCAAAGGCTACGGC 60.108 55.000 0.00 0.00 37.82 5.68
2391 3714 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
2392 3715 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
2393 3716 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
2394 3717 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
2395 3718 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
2396 3719 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
2404 3727 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
2406 3729 2.633488 GTGGAGATCACCAAAGGCTAC 58.367 52.381 13.92 0.00 41.87 3.58
2407 3730 2.027192 GTGGAGATCACCAAAGGCTACA 60.027 50.000 13.92 0.00 41.87 2.74
2408 3731 2.237143 TGGAGATCACCAAAGGCTACAG 59.763 50.000 9.69 0.00 36.96 2.74
2409 3732 2.284190 GAGATCACCAAAGGCTACAGC 58.716 52.381 0.00 0.00 41.14 4.40
2430 3753 3.017581 CCCCCTTCCCTGGTGGAG 61.018 72.222 0.00 0.00 46.24 3.86
2431 3754 2.124996 CCCCTTCCCTGGTGGAGA 59.875 66.667 0.00 0.00 46.24 3.71
2432 3755 1.308216 CCCCTTCCCTGGTGGAGAT 60.308 63.158 0.00 0.00 46.24 2.75
2433 3756 1.348775 CCCCTTCCCTGGTGGAGATC 61.349 65.000 0.00 0.00 46.24 2.75
2434 3757 0.621571 CCCTTCCCTGGTGGAGATCA 60.622 60.000 0.00 0.00 46.24 2.92
2435 3758 0.543749 CCTTCCCTGGTGGAGATCAC 59.456 60.000 0.00 0.00 46.24 3.06
2443 3766 3.965888 GTGGAGATCACCAAAGGCT 57.034 52.632 13.92 0.00 41.87 4.58
2522 3848 4.552166 TCAGCTAACAACAAGAAGCAAC 57.448 40.909 0.00 0.00 37.44 4.17
2523 3849 3.944650 TCAGCTAACAACAAGAAGCAACA 59.055 39.130 0.00 0.00 37.44 3.33
2524 3850 4.397730 TCAGCTAACAACAAGAAGCAACAA 59.602 37.500 0.00 0.00 37.44 2.83
2525 3851 4.736793 CAGCTAACAACAAGAAGCAACAAG 59.263 41.667 0.00 0.00 37.44 3.16
2526 3852 4.640201 AGCTAACAACAAGAAGCAACAAGA 59.360 37.500 0.00 0.00 37.44 3.02
2527 3853 4.972440 GCTAACAACAAGAAGCAACAAGAG 59.028 41.667 0.00 0.00 35.05 2.85
2528 3854 5.449177 GCTAACAACAAGAAGCAACAAGAGT 60.449 40.000 0.00 0.00 35.05 3.24
2529 3855 4.361451 ACAACAAGAAGCAACAAGAGTG 57.639 40.909 0.00 0.00 0.00 3.51
2591 3918 4.260294 GCGCTTCAGAAAATCTCATCTCAG 60.260 45.833 0.00 0.00 0.00 3.35
2613 3940 0.624795 AGACCAATTCCCTCCCTCCC 60.625 60.000 0.00 0.00 0.00 4.30
2646 3973 2.425143 TGAAGGAATGGCACCTCATC 57.575 50.000 0.00 0.00 36.67 2.92
2656 3983 1.001378 GGCACCTCATCACACAAACAC 60.001 52.381 0.00 0.00 0.00 3.32
2671 3998 0.322546 AACACGCTCCCCTCCATTTC 60.323 55.000 0.00 0.00 0.00 2.17
2940 4291 2.032071 GACCACCGAACCCACCTG 59.968 66.667 0.00 0.00 0.00 4.00
2941 4292 4.265056 ACCACCGAACCCACCTGC 62.265 66.667 0.00 0.00 0.00 4.85
2956 4307 4.858680 TGCGCCACGACCACCAAA 62.859 61.111 4.18 0.00 0.00 3.28
2957 4308 4.322385 GCGCCACGACCACCAAAC 62.322 66.667 0.00 0.00 0.00 2.93
2958 4309 3.656045 CGCCACGACCACCAAACC 61.656 66.667 0.00 0.00 0.00 3.27
2959 4310 3.292159 GCCACGACCACCAAACCC 61.292 66.667 0.00 0.00 0.00 4.11
2960 4311 2.193517 CCACGACCACCAAACCCA 59.806 61.111 0.00 0.00 0.00 4.51
2961 4312 2.190841 CCACGACCACCAAACCCAC 61.191 63.158 0.00 0.00 0.00 4.61
2962 4313 2.190841 CACGACCACCAAACCCACC 61.191 63.158 0.00 0.00 0.00 4.61
2963 4314 2.975799 CGACCACCAAACCCACCG 60.976 66.667 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.446272 GCTGTCTGTGTCGCTACCC 60.446 63.158 0.00 0.00 0.00 3.69
104 105 3.908081 CATCCATGCCCGGCTTGC 61.908 66.667 17.91 0.00 33.27 4.01
194 195 1.384502 TGGATAGCTGGAGGGTGGG 60.385 63.158 0.00 0.00 0.00 4.61
304 322 3.764237 ATAACCGTACCCATCCATGAC 57.236 47.619 0.00 0.00 0.00 3.06
310 328 6.854892 CGATCGATATTATAACCGTACCCATC 59.145 42.308 10.26 0.00 0.00 3.51
315 333 6.023435 TGCACGATCGATATTATAACCGTAC 58.977 40.000 24.34 0.00 0.00 3.67
321 339 6.090783 GTGACCTGCACGATCGATATTATAA 58.909 40.000 24.34 0.00 37.83 0.98
468 486 0.249953 TCTTGAACTTGCCGCCGTAA 60.250 50.000 0.00 0.00 0.00 3.18
510 528 1.213537 CTTGAACTTGCCGCCATGG 59.786 57.895 7.63 7.63 42.50 3.66
617 644 2.427453 ACATTAGTTCACTCCGCTCGAT 59.573 45.455 0.00 0.00 0.00 3.59
623 650 4.093408 CCAACATCACATTAGTTCACTCCG 59.907 45.833 0.00 0.00 0.00 4.63
716 743 8.912658 CGCACAGAACGAACTTATTATACATAT 58.087 33.333 0.00 0.00 0.00 1.78
717 744 7.096353 GCGCACAGAACGAACTTATTATACATA 60.096 37.037 0.30 0.00 0.00 2.29
718 745 6.292168 GCGCACAGAACGAACTTATTATACAT 60.292 38.462 0.30 0.00 0.00 2.29
719 746 5.005012 GCGCACAGAACGAACTTATTATACA 59.995 40.000 0.30 0.00 0.00 2.29
720 747 5.421203 GCGCACAGAACGAACTTATTATAC 58.579 41.667 0.30 0.00 0.00 1.47
721 748 4.205588 CGCGCACAGAACGAACTTATTATA 59.794 41.667 8.75 0.00 0.00 0.98
722 749 3.000078 CGCGCACAGAACGAACTTATTAT 60.000 43.478 8.75 0.00 0.00 1.28
723 750 2.343246 CGCGCACAGAACGAACTTATTA 59.657 45.455 8.75 0.00 0.00 0.98
724 751 1.126113 CGCGCACAGAACGAACTTATT 59.874 47.619 8.75 0.00 0.00 1.40
725 752 0.713883 CGCGCACAGAACGAACTTAT 59.286 50.000 8.75 0.00 0.00 1.73
726 753 1.882682 GCGCGCACAGAACGAACTTA 61.883 55.000 29.10 0.00 0.00 2.24
727 754 2.928361 CGCGCACAGAACGAACTT 59.072 55.556 8.75 0.00 0.00 2.66
728 755 3.702555 GCGCGCACAGAACGAACT 61.703 61.111 29.10 0.00 0.00 3.01
729 756 3.995669 TGCGCGCACAGAACGAAC 61.996 61.111 33.09 0.00 0.00 3.95
739 766 0.316442 GTAGACTATACGTGCGCGCA 60.316 55.000 33.09 33.09 42.83 6.09
752 779 4.438336 CCGACATTCACATGTACGTAGACT 60.438 45.833 0.00 0.00 44.22 3.24
753 780 3.789756 CCGACATTCACATGTACGTAGAC 59.210 47.826 0.00 0.00 44.22 2.59
754 781 3.441222 ACCGACATTCACATGTACGTAGA 59.559 43.478 0.00 0.00 44.22 2.59
755 782 3.766151 ACCGACATTCACATGTACGTAG 58.234 45.455 0.00 0.00 44.22 3.51
756 783 3.728566 CGACCGACATTCACATGTACGTA 60.729 47.826 0.00 0.00 44.22 3.57
757 784 2.602878 GACCGACATTCACATGTACGT 58.397 47.619 0.00 0.00 44.22 3.57
758 785 1.582052 CGACCGACATTCACATGTACG 59.418 52.381 0.00 0.00 44.22 3.67
759 786 1.323534 GCGACCGACATTCACATGTAC 59.676 52.381 0.00 0.00 44.22 2.90
760 787 1.635844 GCGACCGACATTCACATGTA 58.364 50.000 0.00 0.00 44.22 2.29
762 789 1.075979 TCGCGACCGACATTCACATG 61.076 55.000 3.71 0.00 38.82 3.21
777 804 1.913403 GACCAAGCAAATTTCATCGCG 59.087 47.619 0.00 0.00 0.00 5.87
783 810 1.418373 GTGCGGACCAAGCAAATTTC 58.582 50.000 0.00 0.00 46.97 2.17
784 811 0.318614 CGTGCGGACCAAGCAAATTT 60.319 50.000 0.00 0.00 46.97 1.82
785 812 1.285641 CGTGCGGACCAAGCAAATT 59.714 52.632 0.00 0.00 46.97 1.82
839 891 2.421073 TGGTTACAGATCGACCGTACAG 59.579 50.000 0.00 0.00 36.22 2.74
846 898 0.989890 GCACGTGGTTACAGATCGAC 59.010 55.000 18.88 0.00 0.00 4.20
859 911 3.055591 TGCATGTTTAAATTGGCACGTG 58.944 40.909 12.28 12.28 0.00 4.49
893 945 8.400947 GGGAGCACGTTCGTATTTATAGATATA 58.599 37.037 0.00 0.00 0.00 0.86
894 946 7.094075 TGGGAGCACGTTCGTATTTATAGATAT 60.094 37.037 0.00 0.00 0.00 1.63
895 947 6.207221 TGGGAGCACGTTCGTATTTATAGATA 59.793 38.462 0.00 0.00 0.00 1.98
914 1001 2.771762 AGGAGAGGGCATGGGAGC 60.772 66.667 0.00 0.00 0.00 4.70
922 1018 0.392327 GTCTGAAAGCAGGAGAGGGC 60.392 60.000 0.00 0.00 42.53 5.19
957 1054 3.630312 GTGTGCACAAAGAAGGGAAACTA 59.370 43.478 23.59 0.00 0.00 2.24
1029 1144 0.235144 CCTCGTACTCGTAGCCATCG 59.765 60.000 0.00 0.00 38.33 3.84
1080 1195 1.900351 CCATCGGCAGGTGAAGAGA 59.100 57.895 0.00 0.00 0.00 3.10
1107 1222 2.378038 GCCTTGATTGGTCTGGCATTA 58.622 47.619 0.00 0.00 41.21 1.90
1157 1272 7.045416 TGATGAAGGTACGTAGCAATTATTGT 58.955 34.615 25.28 0.35 0.00 2.71
1162 1277 5.234329 CGATTGATGAAGGTACGTAGCAATT 59.766 40.000 25.28 12.67 0.00 2.32
1163 1278 4.745125 CGATTGATGAAGGTACGTAGCAAT 59.255 41.667 25.28 14.90 0.00 3.56
1166 1281 3.961182 TCGATTGATGAAGGTACGTAGC 58.039 45.455 16.85 16.85 0.00 3.58
1169 1284 2.427453 AGCTCGATTGATGAAGGTACGT 59.573 45.455 0.00 0.00 0.00 3.57
1171 1286 3.799420 GTCAGCTCGATTGATGAAGGTAC 59.201 47.826 3.45 0.00 34.00 3.34
1185 1300 4.026145 GCTTTAGCTTAATCAGTCAGCTCG 60.026 45.833 0.00 0.00 43.03 5.03
1223 1339 4.552767 GCATACGTCCATCAATAGTGTTGC 60.553 45.833 0.00 0.00 0.00 4.17
1229 1345 3.995199 ACCTGCATACGTCCATCAATAG 58.005 45.455 0.00 0.00 0.00 1.73
1237 1357 1.477030 CGCGTAACCTGCATACGTCC 61.477 60.000 17.06 3.84 45.87 4.79
2026 3333 2.751913 CGTCAGTCGTCCCTCTCGG 61.752 68.421 0.00 0.00 34.52 4.63
2027 3334 2.785921 CGTCAGTCGTCCCTCTCG 59.214 66.667 0.00 0.00 34.52 4.04
2028 3335 2.486042 GCGTCAGTCGTCCCTCTC 59.514 66.667 0.00 0.00 42.13 3.20
2029 3336 3.063084 GGCGTCAGTCGTCCCTCT 61.063 66.667 0.00 0.00 42.13 3.69
2030 3337 3.053849 GAGGCGTCAGTCGTCCCTC 62.054 68.421 0.52 0.00 46.16 4.30
2031 3338 3.063084 GAGGCGTCAGTCGTCCCT 61.063 66.667 0.52 0.00 46.16 4.20
2055 3362 2.887152 GTTCTATGGATGATGGGTTGCC 59.113 50.000 0.00 0.00 0.00 4.52
2104 3416 6.609237 ATTAATGTTCATGGATCACTGTCG 57.391 37.500 0.00 0.00 0.00 4.35
2137 3449 6.885952 AGTATGTATAGCTGGAGTGTACAG 57.114 41.667 0.00 0.00 38.95 2.74
2220 3543 4.142730 GGCAATGCTGAGAAACTAGAGTTG 60.143 45.833 4.82 0.00 38.44 3.16
2268 3591 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
2269 3592 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
2270 3593 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
2271 3594 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
2272 3595 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
2307 3630 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
2308 3631 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
2309 3632 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
2310 3633 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
2311 3634 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
2323 3646 1.222113 GAAGTGGGGAGGCTGTAGC 59.778 63.158 0.00 0.00 41.14 3.58
2324 3647 1.627297 GGGAAGTGGGGAGGCTGTAG 61.627 65.000 0.00 0.00 0.00 2.74
2325 3648 1.615424 GGGAAGTGGGGAGGCTGTA 60.615 63.158 0.00 0.00 0.00 2.74
2386 3709 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
2387 3710 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
2388 3711 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
2389 3712 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
2390 3713 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
2425 3748 2.027192 TGTAGCCTTTGGTGATCTCCAC 60.027 50.000 16.01 5.14 44.95 4.02
2426 3749 2.237143 CTGTAGCCTTTGGTGATCTCCA 59.763 50.000 12.50 12.50 35.49 3.86
2427 3750 2.911484 CTGTAGCCTTTGGTGATCTCC 58.089 52.381 6.88 6.88 0.00 3.71
2428 3751 2.284190 GCTGTAGCCTTTGGTGATCTC 58.716 52.381 0.00 0.00 34.31 2.75
2429 3752 2.409948 GCTGTAGCCTTTGGTGATCT 57.590 50.000 0.00 0.00 34.31 2.75
2441 3764 0.107643 GAATCAGGGGAGGCTGTAGC 59.892 60.000 0.00 0.00 41.14 3.58
2442 3765 1.500474 TGAATCAGGGGAGGCTGTAG 58.500 55.000 0.00 0.00 0.00 2.74
2443 3766 1.965414 TTGAATCAGGGGAGGCTGTA 58.035 50.000 0.00 0.00 0.00 2.74
2444 3767 1.302907 ATTGAATCAGGGGAGGCTGT 58.697 50.000 0.00 0.00 0.00 4.40
2481 3807 0.743688 TTTGTGGCATGTTGCTTCGT 59.256 45.000 0.00 0.00 44.28 3.85
2522 3848 4.614535 GCTGGTTTATGTCTTGCACTCTTG 60.615 45.833 0.00 0.00 0.00 3.02
2523 3849 3.503748 GCTGGTTTATGTCTTGCACTCTT 59.496 43.478 0.00 0.00 0.00 2.85
2524 3850 3.077359 GCTGGTTTATGTCTTGCACTCT 58.923 45.455 0.00 0.00 0.00 3.24
2525 3851 2.162408 GGCTGGTTTATGTCTTGCACTC 59.838 50.000 0.00 0.00 0.00 3.51
2526 3852 2.162681 GGCTGGTTTATGTCTTGCACT 58.837 47.619 0.00 0.00 0.00 4.40
2527 3853 1.885887 TGGCTGGTTTATGTCTTGCAC 59.114 47.619 0.00 0.00 0.00 4.57
2528 3854 2.284754 TGGCTGGTTTATGTCTTGCA 57.715 45.000 0.00 0.00 0.00 4.08
2529 3855 3.243704 TGTTTGGCTGGTTTATGTCTTGC 60.244 43.478 0.00 0.00 0.00 4.01
2591 3918 2.640332 GGAGGGAGGGAATTGGTCTATC 59.360 54.545 0.00 0.00 0.00 2.08
2613 3940 0.025001 CCTTCATTTGCGACGTAGCG 59.975 55.000 15.98 4.09 40.67 4.26
2646 3973 1.507141 GAGGGGAGCGTGTTTGTGTG 61.507 60.000 0.00 0.00 0.00 3.82
2656 3983 0.536006 GATGGAAATGGAGGGGAGCG 60.536 60.000 0.00 0.00 0.00 5.03
2671 3998 2.092212 AGAAGGTAGCATTGGGTGATGG 60.092 50.000 0.00 0.00 0.00 3.51
2714 4041 9.091784 CTGACCTATATTAATTGGATGACGATG 57.908 37.037 0.00 0.00 32.84 3.84
2940 4291 4.322385 GTTTGGTGGTCGTGGCGC 62.322 66.667 0.00 0.00 0.00 6.53
2941 4292 3.656045 GGTTTGGTGGTCGTGGCG 61.656 66.667 0.00 0.00 0.00 5.69
2942 4293 3.292159 GGGTTTGGTGGTCGTGGC 61.292 66.667 0.00 0.00 0.00 5.01
2943 4294 2.190841 GTGGGTTTGGTGGTCGTGG 61.191 63.158 0.00 0.00 0.00 4.94
2944 4295 2.190841 GGTGGGTTTGGTGGTCGTG 61.191 63.158 0.00 0.00 0.00 4.35
2945 4296 2.193786 GGTGGGTTTGGTGGTCGT 59.806 61.111 0.00 0.00 0.00 4.34
2946 4297 2.975799 CGGTGGGTTTGGTGGTCG 60.976 66.667 0.00 0.00 0.00 4.79
2947 4298 3.292159 GCGGTGGGTTTGGTGGTC 61.292 66.667 0.00 0.00 0.00 4.02
2948 4299 4.906537 GGCGGTGGGTTTGGTGGT 62.907 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.