Multiple sequence alignment - TraesCS5A01G316800

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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 TraesCS5A01G316800 chr5A 100.000 2870 0 0 1 2870 527906823 527903954 0.000000e+00 5301.0
1 TraesCS5A01G316800 chr5D 89.764 2755 82 68 61 2718 415274247 415271596 0.000000e+00 3341.0
2 TraesCS5A01G316800 chr5B 88.708 2391 88 69 538 2870 501465488 501463222 0.000000e+00 2752.0
3 TraesCS5A01G316800 chr5B 87.978 549 30 13 1 516 501466618 501466073 1.460000e-172 616.0
4 TraesCS5A01G316800 chr2D 81.423 253 42 3 1077 1325 492676519 492676770 4.850000e-48 202.0
5 TraesCS5A01G316800 chr2B 81.423 253 42 3 1077 1325 578605294 578605545 4.850000e-48 202.0
6 TraesCS5A01G316800 chr2A 83.186 226 31 5 1077 1297 637984706 637984929 1.740000e-47 200.0
7 TraesCS5A01G316800 chr6D 88.000 50 6 0 2776 2825 28059434 28059483 3.090000e-05 60.2


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 TraesCS5A01G316800 chr5A 527903954 527906823 2869 True 5301 5301 100.000 1 2870 1 chr5A.!!$R1 2869
1 TraesCS5A01G316800 chr5D 415271596 415274247 2651 True 3341 3341 89.764 61 2718 1 chr5D.!!$R1 2657
2 TraesCS5A01G316800 chr5B 501463222 501466618 3396 True 1684 2752 88.343 1 2870 2 chr5B.!!$R1 2869

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
423 466 0.034896 AGTCCCAGCTAACCAACACG 59.965 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2813 0.250467 AAATGGCGTGCTGACTGACT 60.25 50.0 0.0 0.0 0.0 3.41 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
23 24 2.209838 AAGTACCGATGATCACTGCG 57.790 50.000 0.00 2.25 0.00 5.18
33 34 2.271607 GATCACTGCGAGCGTCCAGA 62.272 60.000 7.40 0.00 33.40 3.86
39 40 2.807045 CGAGCGTCCAGACACTGC 60.807 66.667 0.00 0.00 0.00 4.40
54 55 4.127171 GACACTGCACTAAGGTCAAAAGA 58.873 43.478 0.00 0.00 0.00 2.52
58 59 4.245660 CTGCACTAAGGTCAAAAGATCGA 58.754 43.478 0.00 0.00 0.00 3.59
95 96 1.200519 AATAGAAGCGGCAGTACCCA 58.799 50.000 1.45 0.00 33.26 4.51
174 194 4.760047 GGGACACGAGCCGCACAT 62.760 66.667 0.00 0.00 0.00 3.21
219 239 4.794439 CCGAGATCACCACGCGCA 62.794 66.667 5.73 0.00 0.00 6.09
240 260 3.044305 GCAGTGCACGGTGACTCC 61.044 66.667 18.34 0.00 0.00 3.85
411 442 2.815308 CGATTCCCCGAGTCCCAG 59.185 66.667 0.00 0.00 0.00 4.45
413 444 2.041265 ATTCCCCGAGTCCCAGCT 59.959 61.111 0.00 0.00 0.00 4.24
423 466 0.034896 AGTCCCAGCTAACCAACACG 59.965 55.000 0.00 0.00 0.00 4.49
570 1177 1.055040 GGAGGGATCATGTCAGGAGG 58.945 60.000 0.00 0.00 0.00 4.30
588 1213 1.220206 GAGCAGCTCAGCCTAAGCA 59.780 57.895 18.17 0.00 42.35 3.91
610 1235 2.579684 CTAGGTGCGCTCCCAAGTCC 62.580 65.000 24.18 6.18 0.00 3.85
612 1237 2.435059 GTGCGCTCCCAAGTCCTC 60.435 66.667 9.73 0.00 0.00 3.71
714 1340 4.764679 CTGCACCTACAGCTATAGAGAG 57.235 50.000 0.00 0.00 0.00 3.20
723 1363 5.489792 ACAGCTATAGAGAGAGAGGAGAG 57.510 47.826 3.21 0.00 0.00 3.20
815 1455 3.557264 GCCCCATCCTCCGATTAAACTAG 60.557 52.174 0.00 0.00 0.00 2.57
829 1469 7.016466 CGATTAAACTAGTCCATCGCTAGTAG 58.984 42.308 14.71 0.00 45.78 2.57
830 1470 7.307870 CGATTAAACTAGTCCATCGCTAGTAGT 60.308 40.741 14.71 0.00 45.78 2.73
831 1471 8.915057 ATTAAACTAGTCCATCGCTAGTAGTA 57.085 34.615 0.00 0.40 45.78 1.82
834 1474 4.756135 ACTAGTCCATCGCTAGTAGTAAGC 59.244 45.833 3.48 0.00 44.98 3.09
835 1475 3.552875 AGTCCATCGCTAGTAGTAAGCA 58.447 45.455 0.00 0.00 40.08 3.91
836 1476 3.566322 AGTCCATCGCTAGTAGTAAGCAG 59.434 47.826 0.00 0.00 40.08 4.24
837 1477 3.564644 GTCCATCGCTAGTAGTAAGCAGA 59.435 47.826 0.00 0.00 40.08 4.26
838 1478 4.036498 GTCCATCGCTAGTAGTAAGCAGAA 59.964 45.833 0.00 0.00 40.08 3.02
839 1479 4.827835 TCCATCGCTAGTAGTAAGCAGAAT 59.172 41.667 0.00 0.00 40.08 2.40
840 1480 5.048643 TCCATCGCTAGTAGTAAGCAGAATC 60.049 44.000 0.00 0.00 40.08 2.52
841 1481 4.469625 TCGCTAGTAGTAAGCAGAATCG 57.530 45.455 0.00 0.00 40.08 3.34
859 1503 1.676006 TCGATCGATCACAGCAAGCTA 59.324 47.619 24.40 0.00 0.00 3.32
860 1504 2.049959 CGATCGATCACAGCAAGCTAG 58.950 52.381 24.40 0.45 0.00 3.42
861 1505 1.791785 GATCGATCACAGCAAGCTAGC 59.208 52.381 20.52 6.62 0.00 3.42
862 1506 0.179100 TCGATCACAGCAAGCTAGCC 60.179 55.000 12.13 0.00 34.23 3.93
863 1507 0.179089 CGATCACAGCAAGCTAGCCT 60.179 55.000 12.13 0.00 34.23 4.58
864 1508 1.580815 GATCACAGCAAGCTAGCCTC 58.419 55.000 12.13 0.27 34.23 4.70
865 1509 0.179936 ATCACAGCAAGCTAGCCTCC 59.820 55.000 12.13 0.00 34.23 4.30
866 1510 1.451028 CACAGCAAGCTAGCCTCCC 60.451 63.158 12.13 0.00 34.23 4.30
867 1511 1.920325 ACAGCAAGCTAGCCTCCCA 60.920 57.895 12.13 0.00 34.23 4.37
868 1512 1.153208 CAGCAAGCTAGCCTCCCAG 60.153 63.158 12.13 0.00 34.23 4.45
869 1513 2.515757 GCAAGCTAGCCTCCCAGC 60.516 66.667 12.13 3.01 38.09 4.85
872 1516 2.837291 AGCTAGCCTCCCAGCTCG 60.837 66.667 12.13 0.00 44.83 5.03
873 1517 4.600576 GCTAGCCTCCCAGCTCGC 62.601 72.222 2.29 0.00 43.67 5.03
874 1518 2.837291 CTAGCCTCCCAGCTCGCT 60.837 66.667 0.00 0.00 43.67 4.93
875 1519 2.835431 TAGCCTCCCAGCTCGCTC 60.835 66.667 0.00 0.00 43.67 5.03
876 1520 3.366406 TAGCCTCCCAGCTCGCTCT 62.366 63.158 0.00 0.00 43.67 4.09
895 1539 3.188786 GCACACCTGCGATCCGTC 61.189 66.667 0.00 0.00 32.44 4.79
927 1571 1.616628 TCCTCCTCTTCCCCTTGCC 60.617 63.158 0.00 0.00 0.00 4.52
1033 1697 2.365635 AGGACGGGGACTGGATGG 60.366 66.667 0.00 0.00 40.47 3.51
1137 1801 2.030412 ATGTTCGCCACGCAGACA 59.970 55.556 0.00 0.00 0.00 3.41
1152 1816 4.351054 ACAAAGCTGGAGCCCCGG 62.351 66.667 0.00 0.00 43.38 5.73
1368 2042 5.900425 TGTCTCTACTCTACTACGTACCAG 58.100 45.833 0.00 0.00 0.00 4.00
1527 2215 3.414700 GGAGATAATGCCGGCGCG 61.415 66.667 23.90 0.00 38.08 6.86
1767 2455 2.047274 GCCGAGTACCAGCAGCAA 60.047 61.111 0.00 0.00 0.00 3.91
1886 2574 3.952811 GTGGTCGGTCAAGCACTC 58.047 61.111 0.00 0.00 42.82 3.51
1887 2575 1.069090 GTGGTCGGTCAAGCACTCA 59.931 57.895 0.00 0.00 42.82 3.41
1888 2576 0.531974 GTGGTCGGTCAAGCACTCAA 60.532 55.000 0.00 0.00 42.82 3.02
1889 2577 0.249868 TGGTCGGTCAAGCACTCAAG 60.250 55.000 0.00 0.00 0.00 3.02
1890 2578 1.569479 GGTCGGTCAAGCACTCAAGC 61.569 60.000 0.00 0.00 0.00 4.01
1891 2579 0.880278 GTCGGTCAAGCACTCAAGCA 60.880 55.000 0.00 0.00 36.85 3.91
1892 2580 0.880278 TCGGTCAAGCACTCAAGCAC 60.880 55.000 0.00 0.00 36.85 4.40
1959 2651 2.864968 CTCGTAACACAGAGCACTACC 58.135 52.381 0.00 0.00 0.00 3.18
1965 2657 2.052690 ACAGAGCACTACCGCCGAT 61.053 57.895 0.00 0.00 0.00 4.18
1966 2658 1.299468 CAGAGCACTACCGCCGATC 60.299 63.158 0.00 0.00 0.00 3.69
1967 2659 1.753078 AGAGCACTACCGCCGATCA 60.753 57.895 0.00 0.00 0.00 2.92
1968 2660 1.141019 GAGCACTACCGCCGATCAA 59.859 57.895 0.00 0.00 0.00 2.57
1971 2663 0.529773 GCACTACCGCCGATCAATCA 60.530 55.000 0.00 0.00 0.00 2.57
2040 2742 1.610038 TGGTACGGTGTCAGTGTGTAG 59.390 52.381 0.00 0.00 0.00 2.74
2041 2743 1.610522 GGTACGGTGTCAGTGTGTAGT 59.389 52.381 0.00 0.00 0.00 2.73
2042 2744 2.606308 GGTACGGTGTCAGTGTGTAGTG 60.606 54.545 0.00 0.00 0.00 2.74
2043 2745 1.108776 ACGGTGTCAGTGTGTAGTGT 58.891 50.000 0.00 0.00 0.00 3.55
2044 2746 2.300433 ACGGTGTCAGTGTGTAGTGTA 58.700 47.619 0.00 0.00 0.00 2.90
2110 2812 2.765699 AGTCTCCTCCTTCTCAATCAGC 59.234 50.000 0.00 0.00 0.00 4.26
2111 2813 2.499289 GTCTCCTCCTTCTCAATCAGCA 59.501 50.000 0.00 0.00 0.00 4.41
2112 2814 2.765135 TCTCCTCCTTCTCAATCAGCAG 59.235 50.000 0.00 0.00 0.00 4.24
2113 2815 2.500910 CTCCTCCTTCTCAATCAGCAGT 59.499 50.000 0.00 0.00 0.00 4.40
2143 2845 1.135689 CGCCATTTTTCTTCACCCTCG 60.136 52.381 0.00 0.00 0.00 4.63
2154 2856 1.546961 TCACCCTCGTCCTCTTCTTC 58.453 55.000 0.00 0.00 0.00 2.87
2171 2873 7.360776 CCTCTTCTTCAATTACTTGCTCTTGTC 60.361 40.741 0.00 0.00 32.11 3.18
2179 2881 6.759497 ATTACTTGCTCTTGTCAATTACCC 57.241 37.500 0.00 0.00 0.00 3.69
2207 2912 2.848302 CCGTGTAATCCGTCGAAACTAC 59.152 50.000 0.00 0.00 0.00 2.73
2263 2968 2.315038 GCAAGTGCATGCGACTAGCC 62.315 60.000 18.84 9.62 42.80 3.93
2271 2980 4.225497 GCGACTAGCCAGGCAAAT 57.775 55.556 15.80 0.00 40.81 2.32
2272 2981 3.379650 GCGACTAGCCAGGCAAATA 57.620 52.632 15.80 0.00 40.81 1.40
2273 2982 1.884235 GCGACTAGCCAGGCAAATAT 58.116 50.000 15.80 0.00 40.81 1.28
2299 3008 2.742774 CATGGCTGTTCATCATGCATG 58.257 47.619 21.07 21.07 33.06 4.06
2300 3009 1.107945 TGGCTGTTCATCATGCATGG 58.892 50.000 25.97 11.53 32.64 3.66
2307 3016 0.753848 TCATCATGCATGGTGGCCAG 60.754 55.000 33.82 13.31 39.36 4.85
2338 3047 2.739885 TCTCTCTTCTCTTGCTGTGC 57.260 50.000 0.00 0.00 0.00 4.57
2339 3048 1.966354 TCTCTCTTCTCTTGCTGTGCA 59.034 47.619 0.00 0.00 36.47 4.57
2340 3049 2.566279 TCTCTCTTCTCTTGCTGTGCAT 59.434 45.455 0.00 0.00 38.76 3.96
2341 3050 2.673862 CTCTCTTCTCTTGCTGTGCATG 59.326 50.000 0.00 0.00 38.76 4.06
2356 3065 3.444742 TGTGCATGATCAATTGGTTCCTC 59.555 43.478 5.42 0.00 0.00 3.71
2398 3107 2.224233 CGAGATCATGGCTGACTGGAAT 60.224 50.000 0.00 0.00 33.22 3.01
2399 3108 3.006217 CGAGATCATGGCTGACTGGAATA 59.994 47.826 0.00 0.00 33.22 1.75
2400 3109 4.322574 CGAGATCATGGCTGACTGGAATAT 60.323 45.833 0.00 0.00 33.22 1.28
2401 3110 4.907809 AGATCATGGCTGACTGGAATATG 58.092 43.478 0.00 0.00 33.22 1.78
2406 3115 2.224042 TGGCTGACTGGAATATGTAGCG 60.224 50.000 0.00 0.00 0.00 4.26
2419 3128 3.932545 ATGTAGCGAGCTAGATTGAGG 57.067 47.619 8.68 0.00 29.66 3.86
2430 3139 3.808726 GCTAGATTGAGGAGAAGCATGTG 59.191 47.826 0.00 0.00 0.00 3.21
2459 3168 0.685785 TAGAGAGGTCCAGGCTGCTG 60.686 60.000 9.56 0.00 0.00 4.41
2460 3169 3.007920 AGAGGTCCAGGCTGCTGG 61.008 66.667 9.56 10.65 45.53 4.85
2467 3176 4.357699 CAGGCTGCTGGATCGATC 57.642 61.111 17.36 17.36 0.00 3.69
2488 3197 3.859961 TCGATCAAGATTCTTTCACGAGC 59.140 43.478 11.72 3.30 0.00 5.03
2490 3199 4.259730 CGATCAAGATTCTTTCACGAGCAG 60.260 45.833 0.00 0.00 0.00 4.24
2491 3200 3.329386 TCAAGATTCTTTCACGAGCAGG 58.671 45.455 0.00 0.00 0.00 4.85
2492 3201 3.006859 TCAAGATTCTTTCACGAGCAGGA 59.993 43.478 0.00 0.00 0.00 3.86
2493 3202 3.244033 AGATTCTTTCACGAGCAGGAG 57.756 47.619 0.00 0.00 0.00 3.69
2494 3203 2.828520 AGATTCTTTCACGAGCAGGAGA 59.171 45.455 0.00 0.00 0.00 3.71
2495 3204 3.259374 AGATTCTTTCACGAGCAGGAGAA 59.741 43.478 0.00 0.00 0.00 2.87
2496 3205 2.732412 TCTTTCACGAGCAGGAGAAG 57.268 50.000 0.00 0.00 0.00 2.85
2625 3334 4.362279 CATCCGGCCATTGTTAATTTCAG 58.638 43.478 2.24 0.00 0.00 3.02
2628 3337 2.539476 GGCCATTGTTAATTTCAGGCG 58.461 47.619 0.00 0.00 41.43 5.52
2657 3366 0.731514 CAAGAGACGCGCCGTTTAGA 60.732 55.000 5.73 0.00 41.37 2.10
2702 3415 0.248539 GAGGTCGATCTGTGGCGTAC 60.249 60.000 0.91 0.00 0.00 3.67
2726 3439 5.575157 TGTAGCCTGGATTTTGATAACCAA 58.425 37.500 0.00 0.00 31.85 3.67
2727 3440 6.194235 TGTAGCCTGGATTTTGATAACCAAT 58.806 36.000 0.00 0.00 34.23 3.16
2733 3446 6.127758 CCTGGATTTTGATAACCAATGAACGA 60.128 38.462 0.00 0.00 34.23 3.85
2745 3458 0.824109 ATGAACGATCGCTGGGAGAA 59.176 50.000 16.60 0.00 0.00 2.87
2757 3470 1.962807 CTGGGAGAACATGGCAAAACA 59.037 47.619 0.00 0.00 0.00 2.83
2758 3471 1.686052 TGGGAGAACATGGCAAAACAC 59.314 47.619 0.00 0.00 0.00 3.32
2784 3497 4.713792 TTTTGGGGGCAAATAATGTTGT 57.286 36.364 0.00 0.00 0.00 3.32
2790 3503 3.498082 GGGCAAATAATGTTGTCGTGAC 58.502 45.455 0.00 0.00 33.78 3.67
2791 3504 3.057876 GGGCAAATAATGTTGTCGTGACA 60.058 43.478 0.00 0.00 39.98 3.58
2831 3544 4.622220 GCAAGCATGAAAAATCCATGGAGT 60.622 41.667 21.33 15.80 41.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.150897 TCTTTTGACCTTAGTGCAGTGT 57.849 40.909 3.69 0.00 0.00 3.55
39 40 4.184629 CCCTCGATCTTTTGACCTTAGTG 58.815 47.826 0.00 0.00 0.00 2.74
54 55 3.287867 ACATCAAATCTTGCCCTCGAT 57.712 42.857 0.00 0.00 0.00 3.59
58 59 7.201857 GCTTCTATTTACATCAAATCTTGCCCT 60.202 37.037 0.00 0.00 37.93 5.19
174 194 2.047274 GCTGCTGCCGGTTCTGTA 60.047 61.111 1.90 0.00 0.00 2.74
411 442 3.428282 CGGGGCGTGTTGGTTAGC 61.428 66.667 0.00 0.00 0.00 3.09
570 1177 0.810823 CTGCTTAGGCTGAGCTGCTC 60.811 60.000 28.41 22.38 40.75 4.26
669 1294 1.079543 CGATGGATGGAGCCCGATC 60.080 63.158 0.00 0.00 0.00 3.69
670 1295 3.063526 CGATGGATGGAGCCCGAT 58.936 61.111 0.00 0.00 0.00 4.18
671 1296 3.928779 GCGATGGATGGAGCCCGA 61.929 66.667 0.00 0.00 0.00 5.14
708 1334 4.223953 GTCTCTCCTCTCCTCTCTCTCTA 58.776 52.174 0.00 0.00 0.00 2.43
711 1337 2.127708 GGTCTCTCCTCTCCTCTCTCT 58.872 57.143 0.00 0.00 0.00 3.10
712 1338 1.143073 GGGTCTCTCCTCTCCTCTCTC 59.857 61.905 0.00 0.00 36.25 3.20
714 1340 0.179029 CGGGTCTCTCCTCTCCTCTC 60.179 65.000 0.00 0.00 36.25 3.20
815 1455 3.564644 TCTGCTTACTACTAGCGATGGAC 59.435 47.826 0.00 0.00 41.54 4.02
829 1469 4.290969 TGTGATCGATCGATTCTGCTTAC 58.709 43.478 29.89 15.54 34.60 2.34
830 1470 4.540824 CTGTGATCGATCGATTCTGCTTA 58.459 43.478 29.89 12.40 34.60 3.09
831 1471 3.379240 CTGTGATCGATCGATTCTGCTT 58.621 45.455 29.89 8.52 34.60 3.91
834 1474 2.735823 TGCTGTGATCGATCGATTCTG 58.264 47.619 29.89 25.66 34.60 3.02
835 1475 3.379240 CTTGCTGTGATCGATCGATTCT 58.621 45.455 29.89 10.93 34.60 2.40
836 1476 2.097007 GCTTGCTGTGATCGATCGATTC 60.097 50.000 29.89 24.06 34.60 2.52
837 1477 1.863454 GCTTGCTGTGATCGATCGATT 59.137 47.619 29.89 14.96 34.60 3.34
838 1478 1.068281 AGCTTGCTGTGATCGATCGAT 59.932 47.619 29.76 29.76 37.59 3.59
839 1479 0.457443 AGCTTGCTGTGATCGATCGA 59.543 50.000 21.86 21.86 0.00 3.59
840 1480 2.049959 CTAGCTTGCTGTGATCGATCG 58.950 52.381 20.03 9.36 0.00 3.69
841 1481 1.791785 GCTAGCTTGCTGTGATCGATC 59.208 52.381 18.72 18.72 0.00 3.69
859 1503 4.775977 AGAGCGAGCTGGGAGGCT 62.776 66.667 0.84 0.00 46.11 4.58
860 1504 4.219999 GAGAGCGAGCTGGGAGGC 62.220 72.222 0.84 0.00 0.00 4.70
861 1505 3.898509 CGAGAGCGAGCTGGGAGG 61.899 72.222 0.84 0.00 40.82 4.30
894 1538 1.693627 GAGGAGCTAATGGAGGACGA 58.306 55.000 0.00 0.00 0.00 4.20
895 1539 0.676736 GGAGGAGCTAATGGAGGACG 59.323 60.000 0.00 0.00 0.00 4.79
896 1540 1.967779 GAGGAGGAGCTAATGGAGGAC 59.032 57.143 0.00 0.00 0.00 3.85
927 1571 0.179026 CATGCACCTGATCTGGAGGG 60.179 60.000 24.13 13.70 34.56 4.30
991 1655 2.844362 CTGCTCCATCGCCCCCTA 60.844 66.667 0.00 0.00 0.00 3.53
1368 2042 1.205820 GCACGGCGAAACTAACACC 59.794 57.895 16.62 0.00 0.00 4.16
1767 2455 4.487412 GGGAACGACGACGGCGAT 62.487 66.667 32.70 20.20 44.46 4.58
1885 2573 3.270027 CGATTCCTTGTATGGTGCTTGA 58.730 45.455 0.00 0.00 0.00 3.02
1886 2574 2.223340 GCGATTCCTTGTATGGTGCTTG 60.223 50.000 0.00 0.00 0.00 4.01
1887 2575 2.017049 GCGATTCCTTGTATGGTGCTT 58.983 47.619 0.00 0.00 0.00 3.91
1888 2576 1.668419 GCGATTCCTTGTATGGTGCT 58.332 50.000 0.00 0.00 0.00 4.40
1889 2577 0.663153 GGCGATTCCTTGTATGGTGC 59.337 55.000 0.00 0.00 0.00 5.01
1890 2578 0.937304 CGGCGATTCCTTGTATGGTG 59.063 55.000 0.00 0.00 0.00 4.17
1891 2579 0.828022 TCGGCGATTCCTTGTATGGT 59.172 50.000 4.99 0.00 0.00 3.55
1892 2580 1.217882 GTCGGCGATTCCTTGTATGG 58.782 55.000 14.79 0.00 0.00 2.74
1959 2651 0.937304 ACGGATTTGATTGATCGGCG 59.063 50.000 0.00 0.00 0.00 6.46
1965 2657 4.253685 GTCTTCTCCACGGATTTGATTGA 58.746 43.478 0.00 0.00 0.00 2.57
1966 2658 3.062639 CGTCTTCTCCACGGATTTGATTG 59.937 47.826 0.00 0.00 33.46 2.67
1967 2659 3.056107 TCGTCTTCTCCACGGATTTGATT 60.056 43.478 0.00 0.00 37.85 2.57
1968 2660 2.496070 TCGTCTTCTCCACGGATTTGAT 59.504 45.455 0.00 0.00 37.85 2.57
1971 2663 1.402456 CGTCGTCTTCTCCACGGATTT 60.402 52.381 0.00 0.00 37.85 2.17
2040 2742 3.187700 CTGGGTTTCGAGCTATGTACAC 58.812 50.000 0.00 0.00 0.00 2.90
2041 2743 2.167693 CCTGGGTTTCGAGCTATGTACA 59.832 50.000 0.00 0.00 0.00 2.90
2042 2744 2.167900 ACCTGGGTTTCGAGCTATGTAC 59.832 50.000 0.00 0.00 0.00 2.90
2043 2745 2.429610 GACCTGGGTTTCGAGCTATGTA 59.570 50.000 0.00 0.00 0.00 2.29
2044 2746 1.207329 GACCTGGGTTTCGAGCTATGT 59.793 52.381 0.00 0.00 0.00 2.29
2088 2790 3.430651 GCTGATTGAGAAGGAGGAGACTG 60.431 52.174 0.00 0.00 44.43 3.51
2110 2812 0.952497 AATGGCGTGCTGACTGACTG 60.952 55.000 0.00 0.00 0.00 3.51
2111 2813 0.250467 AAATGGCGTGCTGACTGACT 60.250 50.000 0.00 0.00 0.00 3.41
2112 2814 0.593128 AAAATGGCGTGCTGACTGAC 59.407 50.000 0.00 0.00 0.00 3.51
2113 2815 1.266718 GAAAAATGGCGTGCTGACTGA 59.733 47.619 0.00 0.00 0.00 3.41
2143 2845 6.169800 AGAGCAAGTAATTGAAGAAGAGGAC 58.830 40.000 7.18 0.00 0.00 3.85
2154 2856 7.029563 GGGTAATTGACAAGAGCAAGTAATTG 58.970 38.462 0.00 0.00 29.14 2.32
2171 2873 1.673009 ACGGTGTGGCGGGTAATTG 60.673 57.895 0.00 0.00 0.00 2.32
2179 2881 2.449525 CGGATTACACGGTGTGGCG 61.450 63.158 23.36 5.88 37.94 5.69
2207 2912 8.383619 CGATCTCTATAAGTTTGGTTTTGTGAG 58.616 37.037 0.00 0.00 0.00 3.51
2253 2958 0.539518 TATTTGCCTGGCTAGTCGCA 59.460 50.000 21.03 0.00 41.67 5.10
2254 2959 1.884235 ATATTTGCCTGGCTAGTCGC 58.116 50.000 21.03 0.00 38.13 5.19
2255 2960 3.990092 TGTATATTTGCCTGGCTAGTCG 58.010 45.455 21.03 0.00 0.00 4.18
2256 2961 4.154918 GCATGTATATTTGCCTGGCTAGTC 59.845 45.833 21.03 4.76 32.66 2.59
2263 2968 3.257375 AGCCATGCATGTATATTTGCCTG 59.743 43.478 24.58 6.39 38.08 4.85
2270 2979 5.318630 TGATGAACAGCCATGCATGTATAT 58.681 37.500 24.58 7.38 0.00 0.86
2271 2980 4.716794 TGATGAACAGCCATGCATGTATA 58.283 39.130 24.58 4.93 0.00 1.47
2272 2981 3.558033 TGATGAACAGCCATGCATGTAT 58.442 40.909 24.58 10.33 0.00 2.29
2273 2982 3.002038 TGATGAACAGCCATGCATGTA 57.998 42.857 24.58 3.26 0.00 2.29
2296 3005 3.290710 AGCTTATTAACTGGCCACCATG 58.709 45.455 0.00 0.00 30.82 3.66
2297 3006 3.669939 AGCTTATTAACTGGCCACCAT 57.330 42.857 0.00 0.00 30.82 3.55
2298 3007 3.449746 AAGCTTATTAACTGGCCACCA 57.550 42.857 0.00 0.00 0.00 4.17
2299 3008 4.017126 AGAAAGCTTATTAACTGGCCACC 58.983 43.478 0.00 0.00 0.00 4.61
2300 3009 4.944317 AGAGAAAGCTTATTAACTGGCCAC 59.056 41.667 0.00 0.00 0.00 5.01
2307 3016 8.387354 GCAAGAGAAGAGAGAAAGCTTATTAAC 58.613 37.037 0.00 0.00 0.00 2.01
2338 3047 2.620115 CCCGAGGAACCAATTGATCATG 59.380 50.000 7.12 0.00 0.00 3.07
2339 3048 2.509548 TCCCGAGGAACCAATTGATCAT 59.490 45.455 7.12 2.41 0.00 2.45
2340 3049 1.912731 TCCCGAGGAACCAATTGATCA 59.087 47.619 7.12 0.00 0.00 2.92
2341 3050 2.289565 GTCCCGAGGAACCAATTGATC 58.710 52.381 7.12 4.86 31.38 2.92
2356 3065 0.521291 AATCATTGTGTTGCGTCCCG 59.479 50.000 0.00 0.00 0.00 5.14
2398 3107 4.652822 TCCTCAATCTAGCTCGCTACATA 58.347 43.478 0.00 0.00 0.00 2.29
2399 3108 3.491342 TCCTCAATCTAGCTCGCTACAT 58.509 45.455 0.00 0.00 0.00 2.29
2400 3109 2.881513 CTCCTCAATCTAGCTCGCTACA 59.118 50.000 0.00 0.00 0.00 2.74
2401 3110 3.142951 TCTCCTCAATCTAGCTCGCTAC 58.857 50.000 0.00 0.00 0.00 3.58
2406 3115 4.202243 ACATGCTTCTCCTCAATCTAGCTC 60.202 45.833 0.00 0.00 0.00 4.09
2419 3128 1.467920 CTTTCCCCCACATGCTTCTC 58.532 55.000 0.00 0.00 0.00 2.87
2430 3139 1.124780 GACCTCTCTAGCTTTCCCCC 58.875 60.000 0.00 0.00 0.00 5.40
2461 3170 5.400782 CGTGAAAGAATCTTGATCGATCGAT 59.599 40.000 29.76 29.76 37.59 3.59
2462 3171 4.735338 CGTGAAAGAATCTTGATCGATCGA 59.265 41.667 21.86 21.86 0.00 3.59
2463 3172 4.735338 TCGTGAAAGAATCTTGATCGATCG 59.265 41.667 20.03 9.36 0.00 3.69
2464 3173 5.332205 GCTCGTGAAAGAATCTTGATCGATC 60.332 44.000 18.72 18.72 0.00 3.69
2465 3174 4.505922 GCTCGTGAAAGAATCTTGATCGAT 59.494 41.667 0.00 0.00 0.00 3.59
2466 3175 3.859961 GCTCGTGAAAGAATCTTGATCGA 59.140 43.478 0.00 6.41 0.00 3.59
2467 3176 3.614176 TGCTCGTGAAAGAATCTTGATCG 59.386 43.478 0.00 2.27 0.00 3.69
2488 3197 1.958288 TTCCCCTTCTCCTTCTCCTG 58.042 55.000 0.00 0.00 0.00 3.86
2490 3199 1.414550 CGATTCCCCTTCTCCTTCTCC 59.585 57.143 0.00 0.00 0.00 3.71
2491 3200 2.389715 TCGATTCCCCTTCTCCTTCTC 58.610 52.381 0.00 0.00 0.00 2.87
2492 3201 2.502130 GTTCGATTCCCCTTCTCCTTCT 59.498 50.000 0.00 0.00 0.00 2.85
2493 3202 2.236395 TGTTCGATTCCCCTTCTCCTTC 59.764 50.000 0.00 0.00 0.00 3.46
2494 3203 2.266279 TGTTCGATTCCCCTTCTCCTT 58.734 47.619 0.00 0.00 0.00 3.36
2495 3204 1.952621 TGTTCGATTCCCCTTCTCCT 58.047 50.000 0.00 0.00 0.00 3.69
2496 3205 2.290071 TGTTGTTCGATTCCCCTTCTCC 60.290 50.000 0.00 0.00 0.00 3.71
2625 3334 1.065273 CTCTTGCCATGCATTCGCC 59.935 57.895 11.95 0.00 38.76 5.54
2628 3337 0.248377 GCGTCTCTTGCCATGCATTC 60.248 55.000 0.00 0.00 38.76 2.67
2670 3379 6.498651 ACAGATCGACCTCCCTTTTGATATAT 59.501 38.462 0.00 0.00 0.00 0.86
2671 3380 5.839063 ACAGATCGACCTCCCTTTTGATATA 59.161 40.000 0.00 0.00 0.00 0.86
2672 3381 4.656112 ACAGATCGACCTCCCTTTTGATAT 59.344 41.667 0.00 0.00 0.00 1.63
2702 3415 5.192927 TGGTTATCAAAATCCAGGCTACAG 58.807 41.667 0.00 0.00 0.00 2.74
2726 3439 0.824109 TTCTCCCAGCGATCGTTCAT 59.176 50.000 17.81 0.00 0.00 2.57
2727 3440 0.108804 GTTCTCCCAGCGATCGTTCA 60.109 55.000 17.81 0.00 0.00 3.18
2733 3446 1.153086 GCCATGTTCTCCCAGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
2745 3458 2.663826 AAACGTGTGTTTTGCCATGT 57.336 40.000 0.00 0.00 45.89 3.21
2757 3470 0.833949 ATTTGCCCCCAAAAACGTGT 59.166 45.000 0.00 0.00 43.58 4.49
2758 3471 2.821991 TATTTGCCCCCAAAAACGTG 57.178 45.000 0.00 0.00 43.58 4.49
2767 3480 1.822371 ACGACAACATTATTTGCCCCC 59.178 47.619 0.00 0.00 0.00 5.40
2768 3481 2.490115 TCACGACAACATTATTTGCCCC 59.510 45.455 0.00 0.00 0.00 5.80
2769 3482 3.057876 TGTCACGACAACATTATTTGCCC 60.058 43.478 0.00 0.00 38.56 5.36
2784 3497 6.861055 GCTAAAGAAAATTTCCATTGTCACGA 59.139 34.615 1.57 0.00 29.62 4.35
2790 3503 7.424227 TGCTTGCTAAAGAAAATTTCCATTG 57.576 32.000 1.57 0.00 35.19 2.82
2791 3504 7.879160 TCATGCTTGCTAAAGAAAATTTCCATT 59.121 29.630 1.57 1.29 35.19 3.16
2795 3508 9.934190 TTTTTCATGCTTGCTAAAGAAAATTTC 57.066 25.926 0.00 0.00 35.63 2.17
2799 3512 7.714377 TGGATTTTTCATGCTTGCTAAAGAAAA 59.286 29.630 0.00 0.00 35.19 2.29
2844 3558 2.949447 AGCAAGAACAACAATCCTGGT 58.051 42.857 0.00 0.00 0.00 4.00
2845 3559 5.452078 TTTAGCAAGAACAACAATCCTGG 57.548 39.130 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.