Multiple sequence alignment - TraesCS6A01G168400

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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 TraesCS6A01G168400 chr6A 100.000 4793 0 0 1 4793 174448485 174453277 0.000000e+00 8852
1 TraesCS6A01G168400 chr6A 86.885 2562 275 36 2249 4793 173184871 173187388 0.000000e+00 2813
2 TraesCS6A01G168400 chr6A 87.923 1035 105 15 2249 3271 173316165 173317191 0.000000e+00 1201
3 TraesCS6A01G168400 chr6A 86.823 979 125 4 1146 2122 173183529 173184505 0.000000e+00 1090
4 TraesCS6A01G168400 chr6A 88.639 757 83 3 4038 4793 173426226 173426980 0.000000e+00 918
5 TraesCS6A01G168400 chr6A 88.646 458 42 4 3591 4046 173345169 173345618 2.520000e-152 549
6 TraesCS6A01G168400 chr6A 80.057 707 101 21 1271 1963 173433717 173434397 5.580000e-134 488
7 TraesCS6A01G168400 chr6A 81.993 572 60 9 853 1424 173314855 173315383 3.400000e-121 446
8 TraesCS6A01G168400 chr6A 86.744 347 42 3 3249 3595 173317205 173317547 2.710000e-102 383
9 TraesCS6A01G168400 chr6A 74.462 1069 185 64 3092 4109 173123465 173124496 9.730000e-102 381
10 TraesCS6A01G168400 chr6D 91.442 2559 190 23 2249 4793 133956059 133958602 0.000000e+00 3485
11 TraesCS6A01G168400 chr6D 92.578 1819 118 10 2249 4054 133582392 133584206 0.000000e+00 2595
12 TraesCS6A01G168400 chr6D 92.593 1809 112 11 2256 4054 133883787 133885583 0.000000e+00 2579
13 TraesCS6A01G168400 chr6D 91.684 1443 111 6 819 2254 133882310 133883750 0.000000e+00 1991
14 TraesCS6A01G168400 chr6D 91.256 1441 120 5 819 2254 133580923 133582362 0.000000e+00 1958
15 TraesCS6A01G168400 chr6D 91.048 1441 122 5 819 2257 133954596 133956031 0.000000e+00 1940
16 TraesCS6A01G168400 chr6D 91.946 745 54 6 4052 4793 133894665 133895406 0.000000e+00 1038
17 TraesCS6A01G168400 chr6D 90.769 520 46 2 4274 4792 133705877 133706395 0.000000e+00 693
18 TraesCS6A01G168400 chr6D 80.085 708 85 19 1271 1963 133480581 133481247 4.340000e-130 475
19 TraesCS6A01G168400 chr6D 92.920 226 15 1 4054 4278 133690667 133690892 1.290000e-85 327
20 TraesCS6A01G168400 chr6B 89.845 1999 181 16 2254 4239 232591066 232593055 0.000000e+00 2547
21 TraesCS6A01G168400 chr6B 88.835 1442 152 4 822 2254 232589590 232591031 0.000000e+00 1762
22 TraesCS6A01G168400 chr6B 77.034 1106 145 64 893 1963 232323365 232324396 7.060000e-148 534
23 TraesCS6A01G168400 chr6B 87.032 347 42 3 4269 4614 232593052 232593396 5.820000e-104 388
24 TraesCS6A01G168400 chr7D 93.873 816 50 0 2 817 135494585 135495400 0.000000e+00 1230
25 TraesCS6A01G168400 chr3D 93.765 818 50 1 1 817 261661886 261661069 0.000000e+00 1227
26 TraesCS6A01G168400 chr3D 93.643 818 50 2 1 817 505416738 505417554 0.000000e+00 1221
27 TraesCS6A01G168400 chr3D 93.635 817 51 1 1 817 611392528 611391713 0.000000e+00 1219
28 TraesCS6A01G168400 chr5D 93.560 823 46 5 1 817 495098150 495098971 0.000000e+00 1219
29 TraesCS6A01G168400 chr1D 93.529 819 52 1 1 818 203631680 203630862 0.000000e+00 1218
30 TraesCS6A01G168400 chr1D 93.513 817 53 0 1 817 485801020 485800204 0.000000e+00 1216
31 TraesCS6A01G168400 chr4D 93.423 821 53 1 1 820 282189868 282190688 0.000000e+00 1216
32 TraesCS6A01G168400 chr4D 93.513 817 53 0 1 817 296238728 296239544 0.000000e+00 1216


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 TraesCS6A01G168400 chr6A 174448485 174453277 4792 False 8852.000000 8852 100.000000 1 4793 1 chr6A.!!$F5 4792
1 TraesCS6A01G168400 chr6A 173183529 173187388 3859 False 1951.500000 2813 86.854000 1146 4793 2 chr6A.!!$F6 3647
2 TraesCS6A01G168400 chr6A 173426226 173426980 754 False 918.000000 918 88.639000 4038 4793 1 chr6A.!!$F3 755
3 TraesCS6A01G168400 chr6A 173314855 173317547 2692 False 676.666667 1201 85.553333 853 3595 3 chr6A.!!$F7 2742
4 TraesCS6A01G168400 chr6A 173433717 173434397 680 False 488.000000 488 80.057000 1271 1963 1 chr6A.!!$F4 692
5 TraesCS6A01G168400 chr6A 173123465 173124496 1031 False 381.000000 381 74.462000 3092 4109 1 chr6A.!!$F1 1017
6 TraesCS6A01G168400 chr6D 133954596 133958602 4006 False 2712.500000 3485 91.245000 819 4793 2 chr6D.!!$F7 3974
7 TraesCS6A01G168400 chr6D 133882310 133885583 3273 False 2285.000000 2579 92.138500 819 4054 2 chr6D.!!$F6 3235
8 TraesCS6A01G168400 chr6D 133580923 133584206 3283 False 2276.500000 2595 91.917000 819 4054 2 chr6D.!!$F5 3235
9 TraesCS6A01G168400 chr6D 133894665 133895406 741 False 1038.000000 1038 91.946000 4052 4793 1 chr6D.!!$F4 741
10 TraesCS6A01G168400 chr6D 133705877 133706395 518 False 693.000000 693 90.769000 4274 4792 1 chr6D.!!$F3 518
11 TraesCS6A01G168400 chr6D 133480581 133481247 666 False 475.000000 475 80.085000 1271 1963 1 chr6D.!!$F1 692
12 TraesCS6A01G168400 chr6B 232589590 232593396 3806 False 1565.666667 2547 88.570667 822 4614 3 chr6B.!!$F2 3792
13 TraesCS6A01G168400 chr6B 232323365 232324396 1031 False 534.000000 534 77.034000 893 1963 1 chr6B.!!$F1 1070
14 TraesCS6A01G168400 chr7D 135494585 135495400 815 False 1230.000000 1230 93.873000 2 817 1 chr7D.!!$F1 815
15 TraesCS6A01G168400 chr3D 261661069 261661886 817 True 1227.000000 1227 93.765000 1 817 1 chr3D.!!$R1 816
16 TraesCS6A01G168400 chr3D 505416738 505417554 816 False 1221.000000 1221 93.643000 1 817 1 chr3D.!!$F1 816
17 TraesCS6A01G168400 chr3D 611391713 611392528 815 True 1219.000000 1219 93.635000 1 817 1 chr3D.!!$R2 816
18 TraesCS6A01G168400 chr5D 495098150 495098971 821 False 1219.000000 1219 93.560000 1 817 1 chr5D.!!$F1 816
19 TraesCS6A01G168400 chr1D 203630862 203631680 818 True 1218.000000 1218 93.529000 1 818 1 chr1D.!!$R1 817
20 TraesCS6A01G168400 chr1D 485800204 485801020 816 True 1216.000000 1216 93.513000 1 817 1 chr1D.!!$R2 816
21 TraesCS6A01G168400 chr4D 282189868 282190688 820 False 1216.000000 1216 93.423000 1 820 1 chr4D.!!$F1 819
22 TraesCS6A01G168400 chr4D 296238728 296239544 816 False 1216.000000 1216 93.513000 1 817 1 chr4D.!!$F2 816

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
873 881 1.732259 CGTGGTCAAATAGTCAGGCAC 59.268 52.381 0.0 0.0 0.0 5.01 F
1553 1590 0.098728 CGGCGATGTTTTGGATGGAC 59.901 55.000 0.0 0.0 0.0 4.02 F
2871 3186 0.392998 GGTCACATCGCATTCCCTGT 60.393 55.000 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2427 0.620556 CCATCTAGGTGTGTTGGGCT 59.379 55.000 1.52 0.0 0.00 5.19 R
3273 3635 1.001760 ACCCTGGTAGTCCATCGCT 59.998 57.895 0.00 0.0 43.43 4.93 R
4568 4976 0.112412 ATTTTGTCGCACCCTTCCCT 59.888 50.000 0.00 0.0 0.00 4.20 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
34 35 8.238631 GTGACCTCAAAAACAAAAGTAACTACA 58.761 33.333 0.00 0.00 0.00 2.74
45 46 9.515020 AACAAAAGTAACTACACACAAATGATG 57.485 29.630 0.00 0.00 0.00 3.07
60 61 6.756542 CACAAATGATGAACATGCTCATGATT 59.243 34.615 16.15 15.73 40.14 2.57
163 164 4.451629 AATCAACACTACTAGTCACCCG 57.548 45.455 0.00 0.00 0.00 5.28
257 258 4.157105 TGCTGTTGAAGATGTTGATGGATG 59.843 41.667 0.00 0.00 0.00 3.51
304 305 7.284820 AGTTGTTGGTGATGATGATGATGATA 58.715 34.615 0.00 0.00 0.00 2.15
632 640 6.858478 GTGAAGTTTTAGCTCATTTGGAGTTC 59.142 38.462 0.00 0.00 45.88 3.01
649 657 4.281435 GGAGTTCTGTAGAATAGGTAGCCC 59.719 50.000 0.00 0.00 36.33 5.19
691 699 2.758979 AGATTTCCAGCTGCCAGAATTG 59.241 45.455 8.66 0.00 0.00 2.32
708 716 5.180117 CAGAATTGTCCCTCTTTGTGTGTAG 59.820 44.000 0.00 0.00 0.00 2.74
820 828 3.149981 TGCAAAATGGACGTATCACCAA 58.850 40.909 0.00 0.00 39.69 3.67
829 837 3.318275 GGACGTATCACCAAGCAGATAGA 59.682 47.826 0.00 0.00 0.00 1.98
854 862 9.490663 GAATTTCCATTCATTTCTTAGTACACG 57.509 33.333 0.00 0.00 39.03 4.49
858 866 5.642063 CCATTCATTTCTTAGTACACGTGGT 59.358 40.000 21.57 8.16 0.00 4.16
873 881 1.732259 CGTGGTCAAATAGTCAGGCAC 59.268 52.381 0.00 0.00 0.00 5.01
884 892 2.111043 CAGGCACACACGGAACCT 59.889 61.111 0.00 0.00 0.00 3.50
906 914 3.220110 AGACTTGTGAAGACGTACTCCA 58.780 45.455 0.00 0.00 0.00 3.86
914 922 3.285484 GAAGACGTACTCCACCTGGATA 58.715 50.000 0.00 0.00 44.46 2.59
924 932 3.326521 TCCACCTGGATATGTAGCCATT 58.673 45.455 0.00 0.00 41.51 3.16
947 955 4.338118 TCATGGAAAGAAACGCTTGAAACT 59.662 37.500 0.00 0.00 36.80 2.66
988 998 3.744660 TCCTTTTGAACCTCTCTGCTTC 58.255 45.455 0.00 0.00 0.00 3.86
1059 1071 6.087423 CACAGATCTATAGAATTGAAGTCGCG 59.913 42.308 18.51 0.00 0.00 5.87
1062 1074 2.309528 ATAGAATTGAAGTCGCGCCA 57.690 45.000 0.00 0.00 0.00 5.69
1236 1257 3.159213 ACAGGAGGCAACATCATCAAA 57.841 42.857 0.00 0.00 41.41 2.69
1249 1270 7.627726 GCAACATCATCAAAGATGAACATGAGA 60.628 37.037 13.07 0.00 46.51 3.27
1351 1375 2.291043 CGCCACTCACCCCTACCTT 61.291 63.158 0.00 0.00 0.00 3.50
1358 1382 1.978580 CTCACCCCTACCTTGTGAAGT 59.021 52.381 0.00 0.00 38.45 3.01
1465 1493 3.709653 ACCACATCGTCCAGGTATGTAAT 59.290 43.478 5.01 0.00 32.70 1.89
1553 1590 0.098728 CGGCGATGTTTTGGATGGAC 59.901 55.000 0.00 0.00 0.00 4.02
1593 1630 3.943381 AGTCGTCATACCGTGAAGTGATA 59.057 43.478 0.00 0.00 38.90 2.15
1599 1636 4.397103 TCATACCGTGAAGTGATACGAGTT 59.603 41.667 0.00 0.00 42.54 3.01
1613 1650 1.412710 ACGAGTTGCAGAGTTGAAGGA 59.587 47.619 0.00 0.00 0.00 3.36
1657 1694 3.668757 GCAGACGTACGTCATCAACTACA 60.669 47.826 40.48 0.00 46.76 2.74
1660 1697 3.568538 ACGTACGTCATCAACTACAACC 58.431 45.455 16.72 0.00 0.00 3.77
1748 1785 2.359850 GTGCCTGGAATGCGGTCA 60.360 61.111 0.00 0.00 0.00 4.02
1782 1819 1.068954 GCCAACTTCCTCTTTTGCTCG 60.069 52.381 0.00 0.00 0.00 5.03
1828 1865 2.889512 TCTTACTGTTGCCTCTCTGGA 58.110 47.619 0.00 0.00 38.35 3.86
1947 1997 7.654116 GGACAAGATCTAACATTAGAAGGTAGC 59.346 40.741 5.48 0.00 42.55 3.58
1976 2033 6.264292 ACTTTTGTGAAATGTAGCACCACATA 59.736 34.615 0.00 0.00 38.19 2.29
2058 2121 3.454858 ACTCCATCTATCCAGGTGTGTT 58.545 45.455 0.00 0.00 30.16 3.32
2122 2185 4.869861 GCCCAAAATTATTGTTGTAGCCAG 59.130 41.667 0.00 0.00 0.00 4.85
2142 2408 4.171005 CAGTTAAGACGCACCTAAATCGA 58.829 43.478 0.00 0.00 0.00 3.59
2174 2441 1.906574 CTTAGGAGCCCAACACACCTA 59.093 52.381 0.00 0.00 32.90 3.08
2195 2462 5.043732 CCTAGATGGAGGGAGTAGTGGATAT 60.044 48.000 0.00 0.00 38.35 1.63
2199 2466 3.467483 TGGAGGGAGTAGTGGATATGACT 59.533 47.826 0.00 0.00 0.00 3.41
2217 2484 3.585289 TGACTGGGATGCAAACCTAACTA 59.415 43.478 10.88 0.00 0.00 2.24
2250 2517 1.271871 CCACCTAGTTCACAATGGGCA 60.272 52.381 0.00 0.00 0.00 5.36
2290 2592 4.095410 TCCATTGCGAGCACTATTTTTG 57.905 40.909 0.00 0.00 0.00 2.44
2297 2603 2.348666 CGAGCACTATTTTTGTCCTCCG 59.651 50.000 0.00 0.00 0.00 4.63
2300 2606 2.418976 GCACTATTTTTGTCCTCCGGTC 59.581 50.000 0.00 0.00 0.00 4.79
2317 2623 4.579384 CGCCCACCCAACCAGTGT 62.579 66.667 0.00 0.00 33.20 3.55
2371 2685 4.647615 CGCTACCCCGATCGCCTG 62.648 72.222 10.32 2.24 0.00 4.85
2426 2740 4.295238 CCCTCTATCTATTGGTCCCTCCTA 59.705 50.000 0.00 0.00 37.07 2.94
2502 2816 5.621197 TTCATCAACATGGAAAACGTAGG 57.379 39.130 0.00 0.00 0.00 3.18
2552 2866 2.429250 GCCTTGGTGTAGGTGTTTGTTT 59.571 45.455 0.00 0.00 37.63 2.83
2614 2928 6.827641 TGTGAACAAAATCTAATAGCACGAC 58.172 36.000 0.00 0.00 0.00 4.34
2621 2935 7.012044 ACAAAATCTAATAGCACGACCAATACC 59.988 37.037 0.00 0.00 0.00 2.73
2731 3045 4.236935 CAACACCCACATTCTATGCAAAC 58.763 43.478 0.00 0.00 0.00 2.93
2752 3066 9.414295 GCAAACATATGATTGTATGCATTATGT 57.586 29.630 22.23 8.29 35.87 2.29
2871 3186 0.392998 GGTCACATCGCATTCCCTGT 60.393 55.000 0.00 0.00 0.00 4.00
2895 3211 5.298527 TGAGCAGAGCATATTTTGATCCAAG 59.701 40.000 0.00 0.00 41.83 3.61
2975 3292 5.122512 TGAGCTCAAAGATATACTACCGC 57.877 43.478 15.67 0.00 0.00 5.68
3017 3334 2.350192 CGCGTTTGCTTGTATGGACATA 59.650 45.455 0.00 0.00 39.65 2.29
3108 3425 8.670135 CATGATCAATTATGTTTGCCACATTTT 58.330 29.630 0.00 0.00 44.40 1.82
3225 3542 8.868522 TCTAACTTTCATTGTTGATCCAAGAT 57.131 30.769 0.00 0.00 0.00 2.40
3227 3544 6.906157 ACTTTCATTGTTGATCCAAGATGT 57.094 33.333 0.00 0.00 0.00 3.06
3253 3570 2.117051 GGAAGACCCGGTCCTAGAAAT 58.883 52.381 14.32 0.00 32.18 2.17
3273 3635 7.628234 AGAAATAGAAGAAGAAGATGAAGGCA 58.372 34.615 0.00 0.00 0.00 4.75
3299 3661 2.292918 TGGACTACCAGGGTCTAGCAAT 60.293 50.000 0.00 0.00 41.77 3.56
3387 3749 7.013274 CCTTCTACTGATCTTGGTTGTTTTTCA 59.987 37.037 0.00 0.00 0.00 2.69
3391 3753 7.111247 ACTGATCTTGGTTGTTTTTCATTGA 57.889 32.000 0.00 0.00 0.00 2.57
3481 3862 0.972983 ACCTCTCATGGAGACGGGTG 60.973 60.000 11.48 0.00 44.45 4.61
3496 3877 3.104512 ACGGGTGAAGACTGATATTCCA 58.895 45.455 0.00 0.00 0.00 3.53
3529 3910 0.254178 AATGGTGAGGTAGCTGCCTG 59.746 55.000 29.59 0.00 39.34 4.85
3614 3995 5.874810 GCTCTATTGTCAATGTCTTGGTACA 59.125 40.000 8.39 0.00 32.95 2.90
3654 4040 9.616634 GGATGCTATAATATTGTGTTTGACATG 57.383 33.333 0.00 0.00 33.40 3.21
3749 4136 3.068307 CCTTCGAATCAGAATAGTCCCGT 59.932 47.826 0.00 0.00 0.00 5.28
3876 4270 6.538021 TGACATGGGTTTTCTGTTCAAAAATG 59.462 34.615 0.00 0.00 0.00 2.32
4007 4412 9.802039 ACTTACATGTAGGATTTAGTTTTGGAA 57.198 29.630 20.72 0.00 0.00 3.53
4204 4610 3.432252 GGTTGGTTACGAGTGATGTCAAG 59.568 47.826 0.00 0.00 0.00 3.02
4285 4693 6.723298 TTTTGTGGTTTATATGGCATAGGG 57.277 37.500 13.39 0.00 0.00 3.53
4288 4696 4.079253 GTGGTTTATATGGCATAGGGTGG 58.921 47.826 13.39 0.00 0.00 4.61
4308 4716 2.288886 GGTACCTCGGTCTATTGGATGC 60.289 54.545 4.06 0.00 0.00 3.91
4437 4845 5.200483 GAGGACATTCCCACCAAATATTCA 58.800 41.667 0.00 0.00 37.19 2.57
4487 4895 5.221904 TGCAAGCTATAATCCTGGAATGCTA 60.222 40.000 0.00 0.00 0.00 3.49
4496 4904 0.034186 CTGGAATGCTAAGGGTGGCA 60.034 55.000 0.00 0.00 46.26 4.92
4523 4931 3.189921 GCAATCATGGAGTGCGCA 58.810 55.556 5.66 5.66 43.33 6.09
4529 4937 2.031919 ATGGAGTGCGCAACGGAA 59.968 55.556 14.00 0.00 0.00 4.30
4541 4949 1.135402 GCAACGGAATTGATGGTGGTC 60.135 52.381 0.00 0.00 41.23 4.02
4591 4999 2.231235 GGAAGGGTGCGACAAAATTCAT 59.769 45.455 0.00 0.00 0.00 2.57
4614 5022 3.219281 TCGATACCCGATGAGAATGACA 58.781 45.455 0.00 0.00 43.23 3.58
4662 5070 1.133668 CATTGGGGGAGAGGATGGTTC 60.134 57.143 0.00 0.00 0.00 3.62
4669 5077 1.484240 GGAGAGGATGGTTCTGGAGTG 59.516 57.143 0.00 0.00 0.00 3.51
4672 5080 1.211457 GAGGATGGTTCTGGAGTGCAT 59.789 52.381 0.00 0.00 0.00 3.96
4700 5108 4.974645 AGTCACATCCTTCCACACTTTA 57.025 40.909 0.00 0.00 0.00 1.85
4721 5129 1.893786 CTTGACTCTCCCACTCCCG 59.106 63.158 0.00 0.00 0.00 5.14
4757 5171 9.716556 AATTCACTTTAGACCTTAGAGATAGGA 57.283 33.333 0.00 0.00 36.58 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.184287 TCATGAGCATGTTCATCATTTGTGT 59.816 36.000 20.80 0.00 39.72 3.72
45 46 5.609423 ACTCCTCTAATCATGAGCATGTTC 58.391 41.667 10.01 2.05 39.72 3.18
84 85 9.699410 TTGGTGGAAGATTATATGTTCAAATCT 57.301 29.630 0.00 0.00 40.74 2.40
163 164 3.248602 CGGAACTATAGATTGGTGCTTGC 59.751 47.826 6.78 0.00 0.00 4.01
257 258 1.380380 CCATCTTGGGGAGGGCAAC 60.380 63.158 0.00 0.00 39.12 4.17
442 448 4.938226 GTGCCCATCTTCTGGTATATAAGC 59.062 45.833 0.00 0.00 44.30 3.09
632 640 3.220110 TGTCGGGCTACCTATTCTACAG 58.780 50.000 0.00 0.00 33.28 2.74
649 657 3.334691 TGGACCTGAAAAAGCTATGTCG 58.665 45.455 0.00 0.00 0.00 4.35
691 699 2.808543 CAAGCTACACACAAAGAGGGAC 59.191 50.000 0.00 0.00 0.00 4.46
708 716 6.148264 GCCTTTTCTCTCATAATATGCAAGC 58.852 40.000 0.00 0.00 0.00 4.01
820 828 8.763984 AGAAATGAATGGAAATTCTATCTGCT 57.236 30.769 0.00 0.00 0.00 4.24
829 837 9.010029 ACGTGTACTAAGAAATGAATGGAAATT 57.990 29.630 0.00 0.00 0.00 1.82
854 862 2.484264 GTGTGCCTGACTATTTGACCAC 59.516 50.000 0.00 0.00 0.00 4.16
858 866 2.412870 CGTGTGTGCCTGACTATTTGA 58.587 47.619 0.00 0.00 0.00 2.69
873 881 2.035449 TCACAAGTCTAGGTTCCGTGTG 59.965 50.000 10.17 10.17 36.96 3.82
884 892 4.392047 TGGAGTACGTCTTCACAAGTCTA 58.608 43.478 0.00 0.00 0.00 2.59
906 914 4.263639 CCATGAATGGCTACATATCCAGGT 60.264 45.833 0.00 0.00 41.75 4.00
924 932 4.338118 AGTTTCAAGCGTTTCTTTCCATGA 59.662 37.500 0.00 0.00 31.27 3.07
947 955 7.675161 AAGGAAAGAAAAGAATGGAGGAAAA 57.325 32.000 0.00 0.00 0.00 2.29
988 998 6.895756 TGCTACATATATAGTAGTTGGGAGGG 59.104 42.308 16.76 0.00 40.76 4.30
1059 1071 4.840005 GCTAGAGGTGGCGGTGGC 62.840 72.222 0.00 0.00 38.90 5.01
1179 1195 7.254863 GCAAACACAAGAAAAATGGATCATTGT 60.255 33.333 0.00 0.00 34.04 2.71
1221 1242 4.768448 TGTTCATCTTTGATGATGTTGCCT 59.232 37.500 10.52 0.00 43.03 4.75
1236 1257 2.171237 TGGCCGAATCTCATGTTCATCT 59.829 45.455 0.00 0.00 0.00 2.90
1315 1339 0.946221 CGCACGGCTTGAAGAACTCT 60.946 55.000 0.00 0.00 0.00 3.24
1351 1375 1.137282 TGGTTGCACTCGTACTTCACA 59.863 47.619 0.00 0.00 0.00 3.58
1358 1382 2.343101 GCAGTAATGGTTGCACTCGTA 58.657 47.619 0.00 0.00 40.02 3.43
1465 1493 8.542926 ACACATCAATAATCTAGCCTATATGCA 58.457 33.333 2.72 0.00 0.00 3.96
1487 1515 5.596845 TCTGAATATATTGCGCTACACACA 58.403 37.500 9.73 0.00 0.00 3.72
1553 1590 3.775610 CGACTTTCGAATCTGAAATTGCG 59.224 43.478 0.00 0.00 43.74 4.85
1593 1630 1.412710 TCCTTCAACTCTGCAACTCGT 59.587 47.619 0.00 0.00 0.00 4.18
1599 1636 1.815408 GCCACTTCCTTCAACTCTGCA 60.815 52.381 0.00 0.00 0.00 4.41
1613 1650 2.125512 GCGAGATGTCCGCCACTT 60.126 61.111 0.00 0.00 46.22 3.16
1657 1694 1.637724 TTCAGGAACACCACCCGGTT 61.638 55.000 0.00 0.00 46.31 4.44
1660 1697 1.599797 GGTTCAGGAACACCACCCG 60.600 63.158 13.62 0.00 42.85 5.28
1740 1777 2.680352 ACGAGTCCCTGACCGCAT 60.680 61.111 0.00 0.00 32.50 4.73
1748 1785 4.988716 TGGCGTCCACGAGTCCCT 62.989 66.667 2.58 0.00 43.02 4.20
1782 1819 1.936547 GCATGTACCTTACAGCTCAGC 59.063 52.381 0.00 0.00 42.77 4.26
1791 1828 6.106003 CAGTAAGATGTGTGCATGTACCTTA 58.894 40.000 11.66 8.55 35.07 2.69
1828 1865 7.201821 GCACAAATATGGAAGGTAATAAGTGCT 60.202 37.037 0.00 0.00 41.83 4.40
1874 1911 6.479990 CAGTTAATTGATCTTATCGAGCCACA 59.520 38.462 0.00 0.00 0.00 4.17
1947 1997 7.114811 GTGGTGCTACATTTCACAAAAGTTATG 59.885 37.037 0.00 0.00 35.04 1.90
1976 2033 8.378565 CCATGTCATTTACTACCCTATTCATCT 58.621 37.037 0.00 0.00 0.00 2.90
2029 2092 8.402683 ACACCTGGATAGATGGAGTAGTATTAT 58.597 37.037 0.00 0.00 0.00 1.28
2030 2093 7.670140 CACACCTGGATAGATGGAGTAGTATTA 59.330 40.741 0.00 0.00 0.00 0.98
2042 2105 2.308570 TGCCAAACACACCTGGATAGAT 59.691 45.455 0.00 0.00 34.35 1.98
2122 2185 5.520022 TTTCGATTTAGGTGCGTCTTAAC 57.480 39.130 0.00 0.00 0.00 2.01
2160 2427 0.620556 CCATCTAGGTGTGTTGGGCT 59.379 55.000 1.52 0.00 0.00 5.19
2174 2441 4.358310 TCATATCCACTACTCCCTCCATCT 59.642 45.833 0.00 0.00 0.00 2.90
2195 2462 2.375174 AGTTAGGTTTGCATCCCAGTCA 59.625 45.455 5.09 0.00 0.00 3.41
2199 2466 4.277476 CCATTAGTTAGGTTTGCATCCCA 58.723 43.478 5.09 0.00 0.00 4.37
2250 2517 0.747255 AATCGCAGGCTAGATCGTGT 59.253 50.000 0.00 0.00 0.00 4.49
2300 2606 4.579384 ACACTGGTTGGGTGGGCG 62.579 66.667 0.00 0.00 38.83 6.13
2327 2633 2.121506 ATGGGTGGTGAGGGTGGT 60.122 61.111 0.00 0.00 0.00 4.16
2371 2685 3.207669 CAAGCAGGATGAGCGGCC 61.208 66.667 0.00 0.00 39.69 6.13
2426 2740 4.125239 GGGTACTCCCGACACCTT 57.875 61.111 0.00 0.00 44.74 3.50
2491 2805 6.368213 CACATAAAGACAACCTACGTTTTCC 58.632 40.000 0.00 0.00 30.34 3.13
2502 2816 5.940192 TCACACATCCACATAAAGACAAC 57.060 39.130 0.00 0.00 0.00 3.32
2614 2928 5.334724 ACGACTACTTTACTGGGTATTGG 57.665 43.478 0.00 0.00 0.00 3.16
2621 2935 8.378421 GCTTTACAAATACGACTACTTTACTGG 58.622 37.037 0.00 0.00 0.00 4.00
2684 2998 7.348274 TGTGAAGTTCTCTCCAATATCCCTAAT 59.652 37.037 4.17 0.00 0.00 1.73
2871 3186 4.784177 TGGATCAAAATATGCTCTGCTCA 58.216 39.130 0.00 0.00 0.00 4.26
2910 3226 5.535753 AAAGAACATCCAAAGTCCAAAGG 57.464 39.130 0.00 0.00 0.00 3.11
2966 3283 6.280855 TGCATATGTATTCTGCGGTAGTAT 57.719 37.500 4.29 0.00 38.75 2.12
2972 3289 5.618056 AAGATTGCATATGTATTCTGCGG 57.382 39.130 15.92 0.00 38.75 5.69
2975 3292 6.128822 ACGCGTAAGATTGCATATGTATTCTG 60.129 38.462 11.67 8.08 43.02 3.02
3025 3342 7.710896 ACTGAAAGAAGAAGAAATTGTTCAGG 58.289 34.615 13.01 0.00 37.43 3.86
3160 3477 4.338012 TCCATCAAGCTGACATCAACAAT 58.662 39.130 0.00 0.00 0.00 2.71
3253 3570 4.679106 CGCTGCCTTCATCTTCTTCTTCTA 60.679 45.833 0.00 0.00 0.00 2.10
3273 3635 1.001760 ACCCTGGTAGTCCATCGCT 59.998 57.895 0.00 0.00 43.43 4.93
3368 3730 8.492748 CAATCAATGAAAAACAACCAAGATCAG 58.507 33.333 0.00 0.00 0.00 2.90
3403 3765 3.747099 CGGAAGCAAAACCATGTCTAG 57.253 47.619 0.00 0.00 0.00 2.43
3476 3856 3.819564 TGGAATATCAGTCTTCACCCG 57.180 47.619 0.00 0.00 0.00 5.28
3584 3965 5.494724 AGACATTGACAATAGAGCACACAT 58.505 37.500 0.00 0.00 0.00 3.21
3720 4107 7.417570 GGACTATTCTGATTCGAAGGGTAAAGA 60.418 40.741 3.35 0.00 0.00 2.52
3749 4136 2.360191 GGGAAGGGAGCAATGCCA 59.640 61.111 0.00 0.00 0.00 4.92
3876 4270 7.778470 TTTTTGAACCATTGTAAATGACCAC 57.222 32.000 1.54 0.00 0.00 4.16
3973 4374 5.847111 ATCCTACATGTAAGTTACAGCGA 57.153 39.130 19.87 10.94 42.77 4.93
3974 4375 6.903883 AAATCCTACATGTAAGTTACAGCG 57.096 37.500 19.87 15.44 42.77 5.18
4008 4413 9.912634 CCGGAATTTGCAAAATATTCTACATAT 57.087 29.630 17.19 0.00 0.00 1.78
4122 4528 6.265196 CGGAATTCCCCTCATGATTTTCATTA 59.735 38.462 19.01 0.00 34.28 1.90
4132 4538 1.490490 TCCTTCGGAATTCCCCTCATG 59.510 52.381 19.01 3.71 0.00 3.07
4154 4560 8.421249 AAGCTATATGTGCTAGAAGAAGAGAT 57.579 34.615 0.00 0.00 40.22 2.75
4204 4610 3.930229 TGCAACTTATCGTACACACCATC 59.070 43.478 0.00 0.00 0.00 3.51
4285 4693 2.381911 TCCAATAGACCGAGGTACCAC 58.618 52.381 15.94 7.03 0.00 4.16
4288 4696 2.364324 TGCATCCAATAGACCGAGGTAC 59.636 50.000 0.00 0.00 0.00 3.34
4338 4746 9.812347 TTCCATTGATTATTATAAGAGTGGCAT 57.188 29.630 0.00 0.00 0.00 4.40
4374 4782 9.294030 CTCCACAATTACAAATATCTTCTTTGC 57.706 33.333 0.00 0.00 37.15 3.68
4437 4845 3.367025 CGTTTCGCGTTTCCTCTCTTAAT 59.633 43.478 5.77 0.00 35.54 1.40
4487 4895 0.540365 CCATCACAACTGCCACCCTT 60.540 55.000 0.00 0.00 0.00 3.95
4496 4904 3.021695 CTCCATGATTGCCATCACAACT 58.978 45.455 2.00 0.00 42.46 3.16
4523 4931 1.002659 TCGACCACCATCAATTCCGTT 59.997 47.619 0.00 0.00 0.00 4.44
4529 4937 2.768527 AGTCATCTCGACCACCATCAAT 59.231 45.455 0.00 0.00 46.69 2.57
4541 4949 2.299993 TTGGCAGCTTAGTCATCTCG 57.700 50.000 0.00 0.00 0.00 4.04
4568 4976 0.112412 ATTTTGTCGCACCCTTCCCT 59.888 50.000 0.00 0.00 0.00 4.20
4648 5056 1.127343 CTCCAGAACCATCCTCTCCC 58.873 60.000 0.00 0.00 0.00 4.30
4662 5070 1.147824 CTAGGGCCATGCACTCCAG 59.852 63.158 6.18 0.00 38.16 3.86
4669 5077 0.536006 GGATGTGACTAGGGCCATGC 60.536 60.000 6.18 0.00 0.00 4.06
4672 5080 1.204146 GAAGGATGTGACTAGGGCCA 58.796 55.000 6.18 0.00 0.00 5.36
4700 5108 1.536943 GGAGTGGGAGAGTCAAGCGT 61.537 60.000 0.00 0.00 0.00 5.07
4721 5129 1.055849 AAAGTGAATTGGGTTGGGGC 58.944 50.000 0.00 0.00 0.00 5.80
4769 5183 4.641989 CAGATGGGTTTGGAGGATTAACAG 59.358 45.833 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.