Multiple sequence alignment - TraesCS5D01G106400

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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 TraesCS5D01G106400 chr5D 100.000 6180 0 0 1 6180 119772528 119766349 0.000000e+00 11413
1 TraesCS5D01G106400 chr5D 94.382 178 10 0 3549 3726 508111947 508112124 2.190000e-69 274
2 TraesCS5D01G106400 chr5D 93.452 168 11 0 3559 3726 559427189 559427022 3.700000e-62 250
3 TraesCS5D01G106400 chr5A 95.333 4971 174 30 585 5532 130141529 130136594 0.000000e+00 7841
4 TraesCS5D01G106400 chr5A 96.857 350 6 2 5531 5875 130136511 130136162 1.150000e-161 580
5 TraesCS5D01G106400 chr5A 97.735 309 7 0 5872 6180 130134895 130134587 3.280000e-147 532
6 TraesCS5D01G106400 chr5A 83.060 183 25 6 3 182 492997454 492997633 1.780000e-35 161
7 TraesCS5D01G106400 chr5B 92.484 2049 92 19 585 2591 133015379 133013351 0.000000e+00 2874
8 TraesCS5D01G106400 chr5B 91.711 941 65 8 3729 4657 133012433 133011494 0.000000e+00 1293
9 TraesCS5D01G106400 chr5B 91.718 809 44 13 4686 5477 133011492 133010690 0.000000e+00 1101
10 TraesCS5D01G106400 chr5B 91.760 716 47 10 5473 6180 133010990 133010279 0.000000e+00 985
11 TraesCS5D01G106400 chr5B 95.179 560 22 3 2586 3143 133013324 133012768 0.000000e+00 880
12 TraesCS5D01G106400 chr5B 95.575 339 12 3 3212 3548 133012765 133012428 1.960000e-149 540
13 TraesCS5D01G106400 chr3D 93.945 578 30 3 1 577 554842884 554843457 0.000000e+00 869
14 TraesCS5D01G106400 chr3D 92.358 458 26 6 124 577 372637613 372638065 1.450000e-180 643
15 TraesCS5D01G106400 chr3D 90.704 355 25 5 230 581 305345164 305345513 3.370000e-127 466
16 TraesCS5D01G106400 chr3D 92.000 175 14 0 3551 3725 463808657 463808831 4.780000e-61 246
17 TraesCS5D01G106400 chr1D 92.281 583 34 9 1 577 51552464 51551887 0.000000e+00 817
18 TraesCS5D01G106400 chr7D 91.930 570 34 7 1 567 281085765 281086325 0.000000e+00 787
19 TraesCS5D01G106400 chr7D 91.106 416 29 7 166 577 281086335 281086746 1.950000e-154 556
20 TraesCS5D01G106400 chr7D 91.063 414 29 5 167 577 281086747 281087155 2.520000e-153 553
21 TraesCS5D01G106400 chr6D 91.595 583 28 8 1 580 61736753 61737317 0.000000e+00 785
22 TraesCS5D01G106400 chr7B 91.081 370 24 7 212 577 607952454 607952090 5.570000e-135 492
23 TraesCS5D01G106400 chr2D 94.444 180 9 1 3548 3726 628591802 628591981 6.100000e-70 276
24 TraesCS5D01G106400 chr2D 90.323 186 13 1 3547 3727 634056166 634056351 8.010000e-59 239
25 TraesCS5D01G106400 chr4A 95.322 171 8 0 3556 3726 448515230 448515060 7.890000e-69 272
26 TraesCS5D01G106400 chr4D 94.220 173 8 1 3556 3726 122199877 122200049 4.750000e-66 263
27 TraesCS5D01G106400 chr7A 92.529 174 13 0 3553 3726 469986543 469986370 3.700000e-62 250
28 TraesCS5D01G106400 chr7A 85.443 158 19 4 27 182 561606406 561606251 1.780000e-35 161
29 TraesCS5D01G106400 chr7A 81.667 180 27 5 3 178 672982183 672982006 1.800000e-30 145
30 TraesCS5D01G106400 chr3A 88.158 152 14 4 27 176 661663039 661663188 1.770000e-40 178
31 TraesCS5D01G106400 chr6B 85.443 158 19 4 27 182 142690680 142690525 1.780000e-35 161


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 TraesCS5D01G106400 chr5D 119766349 119772528 6179 True 11413.000000 11413 100.000000 1 6180 1 chr5D.!!$R1 6179
1 TraesCS5D01G106400 chr5A 130134587 130141529 6942 True 2984.333333 7841 96.641667 585 6180 3 chr5A.!!$R1 5595
2 TraesCS5D01G106400 chr5B 133010279 133015379 5100 True 1278.833333 2874 93.071167 585 6180 6 chr5B.!!$R1 5595
3 TraesCS5D01G106400 chr3D 554842884 554843457 573 False 869.000000 869 93.945000 1 577 1 chr3D.!!$F4 576
4 TraesCS5D01G106400 chr1D 51551887 51552464 577 True 817.000000 817 92.281000 1 577 1 chr1D.!!$R1 576
5 TraesCS5D01G106400 chr7D 281085765 281087155 1390 False 632.000000 787 91.366333 1 577 3 chr7D.!!$F1 576
6 TraesCS5D01G106400 chr6D 61736753 61737317 564 False 785.000000 785 91.595000 1 580 1 chr6D.!!$F1 579

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
648 1476 0.179040 TTTGAAGTGACCCACCGGAC 60.179 55.000 9.46 0.0 34.49 4.79 F
1026 1880 0.109735 TGAGTTGCTCGCAGTCGTAG 60.110 55.000 0.00 0.0 36.96 3.51 F
1144 2001 0.248565 GTGATGCTGCTGAGTGGAGA 59.751 55.000 0.00 0.0 36.08 3.71 F
1348 2220 0.739462 CTGTGGCCGCTTACGATCAA 60.739 55.000 18.96 0.0 43.93 2.57 F
1486 2361 1.204704 TGGTTCTGACATACTGGCTCG 59.795 52.381 0.00 0.0 0.00 5.03 F
3314 4227 0.165944 CTAGTTTTGAAGGCCGTGCG 59.834 55.000 0.00 0.0 0.00 5.34 F
4042 4959 0.032130 TCTCAGACCAAGTGTGTCGC 59.968 55.000 0.00 0.0 37.80 5.19 F
4887 5819 2.231235 GGTACGTAAAGGTTCTTCGGGA 59.769 50.000 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 3117 1.154225 GCGACCCAATTGAACAGCG 60.154 57.895 7.12 4.58 0.00 5.18 R
2872 3785 3.201290 ACAGAAGTCTCACTGTTTGCAG 58.799 45.455 6.78 0.00 43.52 4.41 R
3020 3933 4.790718 GATAACCCAGTTATCCCCAACT 57.209 45.455 13.99 0.00 44.84 3.16 R
3314 4227 1.209747 CTAACCTCACTTGTAGGGGGC 59.790 57.143 0.00 0.00 38.54 5.80 R
3633 4548 5.234543 TCAGTGTCGATTAGTCTATGAGTCG 59.765 44.000 0.00 0.00 0.00 4.18 R
4175 5092 0.232816 CGTTAACCGTGGTTCCAACG 59.767 55.000 19.48 19.48 40.85 4.10 R
5091 6039 0.327924 TGATTTGTCAGACCCGCCAT 59.672 50.000 0.00 0.00 0.00 4.40 R
5992 8300 3.898482 ACTATTAATGTGAACCTGGCCC 58.102 45.455 0.00 0.00 0.00 5.80 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
105 106 9.025041 ACAGACCATTGATCATAATATAGACGA 57.975 33.333 0.00 0.00 0.00 4.20
217 623 6.947733 TGATCGGAAATATATTTTCATGCCCT 59.052 34.615 15.35 1.38 0.00 5.19
408 1226 6.435164 ACCCAAGAATTAAATGAGCACCTAT 58.565 36.000 0.00 0.00 0.00 2.57
439 1257 7.426929 AAGCGCAAGAATTATTACCTGATAG 57.573 36.000 11.47 0.00 43.02 2.08
440 1258 6.525629 AGCGCAAGAATTATTACCTGATAGT 58.474 36.000 11.47 0.00 43.02 2.12
441 1259 7.667557 AGCGCAAGAATTATTACCTGATAGTA 58.332 34.615 11.47 0.00 43.02 1.82
460 1278 4.035112 AGTATAAACCGATGAAGTGGGGA 58.965 43.478 0.00 0.00 0.00 4.81
462 1280 1.064825 AAACCGATGAAGTGGGGAGT 58.935 50.000 0.00 0.00 0.00 3.85
507 1328 1.003223 GAAAACAACGAAGGTGGGACG 60.003 52.381 0.00 0.00 0.00 4.79
549 1370 1.396996 CGAAAATTGACCGGCGAAGAT 59.603 47.619 9.30 0.00 0.00 2.40
552 1373 4.260620 CGAAAATTGACCGGCGAAGATTAT 60.261 41.667 9.30 0.00 0.00 1.28
567 1388 6.017934 GCGAAGATTATCAACTGCTCCATTAA 60.018 38.462 0.00 0.00 0.00 1.40
568 1389 7.467267 GCGAAGATTATCAACTGCTCCATTAAA 60.467 37.037 0.00 0.00 0.00 1.52
580 1401 9.606631 AACTGCTCCATTAAAAATAGAGACTAG 57.393 33.333 0.16 0.00 0.00 2.57
581 1402 8.982723 ACTGCTCCATTAAAAATAGAGACTAGA 58.017 33.333 0.00 0.00 0.00 2.43
582 1403 9.474920 CTGCTCCATTAAAAATAGAGACTAGAG 57.525 37.037 0.00 0.00 0.00 2.43
583 1404 9.201989 TGCTCCATTAAAAATAGAGACTAGAGA 57.798 33.333 0.00 0.00 0.00 3.10
621 1442 3.366781 GGCAAGAAATTCTGAGCTTCACC 60.367 47.826 16.57 1.25 31.51 4.02
645 1473 0.240945 GCATTTGAAGTGACCCACCG 59.759 55.000 0.00 0.00 34.49 4.94
648 1476 0.179040 TTTGAAGTGACCCACCGGAC 60.179 55.000 9.46 0.00 34.49 4.79
697 1532 3.303928 CCCTACGGCCCCGATCTC 61.304 72.222 14.44 0.00 42.83 2.75
698 1533 3.671411 CCTACGGCCCCGATCTCG 61.671 72.222 14.44 0.00 42.83 4.04
699 1534 2.593725 CTACGGCCCCGATCTCGA 60.594 66.667 14.44 0.00 43.02 4.04
700 1535 1.972223 CTACGGCCCCGATCTCGAT 60.972 63.158 14.44 0.00 43.02 3.59
701 1536 1.924320 CTACGGCCCCGATCTCGATC 61.924 65.000 14.44 0.00 43.02 3.69
763 1598 1.815003 CGTCATCTCCCATTGCGCA 60.815 57.895 5.66 5.66 0.00 6.09
807 1642 3.775654 CAGCGGTCCTCTCCCCAC 61.776 72.222 0.00 0.00 0.00 4.61
808 1643 3.999285 AGCGGTCCTCTCCCCACT 61.999 66.667 0.00 0.00 0.00 4.00
809 1644 3.462678 GCGGTCCTCTCCCCACTC 61.463 72.222 0.00 0.00 0.00 3.51
810 1645 2.360980 CGGTCCTCTCCCCACTCT 59.639 66.667 0.00 0.00 0.00 3.24
811 1646 1.755008 CGGTCCTCTCCCCACTCTC 60.755 68.421 0.00 0.00 0.00 3.20
812 1647 1.382009 GGTCCTCTCCCCACTCTCC 60.382 68.421 0.00 0.00 0.00 3.71
813 1648 1.755008 GTCCTCTCCCCACTCTCCG 60.755 68.421 0.00 0.00 0.00 4.63
814 1649 1.929088 TCCTCTCCCCACTCTCCGA 60.929 63.158 0.00 0.00 0.00 4.55
815 1650 1.454847 CCTCTCCCCACTCTCCGAG 60.455 68.421 0.00 0.00 35.52 4.63
816 1651 2.043852 TCTCCCCACTCTCCGAGC 60.044 66.667 0.00 0.00 32.04 5.03
817 1652 2.363018 CTCCCCACTCTCCGAGCA 60.363 66.667 0.00 0.00 32.04 4.26
818 1653 1.984570 CTCCCCACTCTCCGAGCAA 60.985 63.158 0.00 0.00 32.04 3.91
938 1792 1.445095 CTCCAGATCCCGAGGCTTG 59.555 63.158 0.00 0.00 0.00 4.01
939 1793 2.037620 CTCCAGATCCCGAGGCTTGG 62.038 65.000 14.36 14.36 0.00 3.61
998 1852 2.507110 TTCGAGTACCTGCTGCCAGC 62.507 60.000 10.45 10.45 42.82 4.85
1020 1874 3.114616 CCGGTGAGTTGCTCGCAG 61.115 66.667 11.14 7.31 42.14 5.18
1022 1876 2.375766 CGGTGAGTTGCTCGCAGTC 61.376 63.158 11.14 0.00 42.14 3.51
1026 1880 0.109735 TGAGTTGCTCGCAGTCGTAG 60.110 55.000 0.00 0.00 36.96 3.51
1033 1890 1.333081 GCTCGCAGTCGTAGTACTAGC 60.333 57.143 1.87 1.88 36.96 3.42
1043 1900 2.543861 CGTAGTACTAGCACATGGGCTG 60.544 54.545 32.71 22.77 45.44 4.85
1049 1906 0.538584 TAGCACATGGGCTGAGTGAG 59.461 55.000 32.71 0.00 45.44 3.51
1132 1989 2.694628 CTCTCTCCTGCTTAGTGATGCT 59.305 50.000 0.00 0.00 0.00 3.79
1133 1990 2.429971 TCTCTCCTGCTTAGTGATGCTG 59.570 50.000 0.00 0.00 0.00 4.41
1136 1993 1.015109 CCTGCTTAGTGATGCTGCTG 58.985 55.000 0.00 0.00 0.00 4.41
1141 1998 2.277969 CTTAGTGATGCTGCTGAGTGG 58.722 52.381 0.00 0.00 0.00 4.00
1142 1999 1.560505 TAGTGATGCTGCTGAGTGGA 58.439 50.000 0.00 0.00 0.00 4.02
1143 2000 0.249676 AGTGATGCTGCTGAGTGGAG 59.750 55.000 0.00 0.00 37.17 3.86
1144 2001 0.248565 GTGATGCTGCTGAGTGGAGA 59.751 55.000 0.00 0.00 36.08 3.71
1145 2002 0.978907 TGATGCTGCTGAGTGGAGAA 59.021 50.000 0.00 0.00 36.08 2.87
1146 2003 1.348696 TGATGCTGCTGAGTGGAGAAA 59.651 47.619 0.00 0.00 36.08 2.52
1147 2004 2.224597 TGATGCTGCTGAGTGGAGAAAA 60.225 45.455 0.00 0.00 36.08 2.29
1148 2005 2.346766 TGCTGCTGAGTGGAGAAAAA 57.653 45.000 0.00 0.00 36.08 1.94
1149 2006 1.949525 TGCTGCTGAGTGGAGAAAAAC 59.050 47.619 0.00 0.00 36.08 2.43
1153 2014 2.807967 TGCTGAGTGGAGAAAAACATCG 59.192 45.455 0.00 0.00 0.00 3.84
1156 2017 3.057019 TGAGTGGAGAAAAACATCGTCG 58.943 45.455 0.00 0.00 0.00 5.12
1164 2030 4.783242 AGAAAAACATCGTCGTGAATTGG 58.217 39.130 0.00 0.00 0.00 3.16
1184 2050 7.943079 ATTGGTCATGACTGATTTGTAATGA 57.057 32.000 24.50 0.00 35.92 2.57
1214 2080 6.739565 GCCATGTTTTTCCTTCTCATCTTGTT 60.740 38.462 0.00 0.00 0.00 2.83
1348 2220 0.739462 CTGTGGCCGCTTACGATCAA 60.739 55.000 18.96 0.00 43.93 2.57
1357 2229 1.934589 CTTACGATCAATGGACGCCA 58.065 50.000 1.01 1.01 38.19 5.69
1486 2361 1.204704 TGGTTCTGACATACTGGCTCG 59.795 52.381 0.00 0.00 0.00 5.03
1676 2551 7.650903 GTCATTGAATTTCTATGGAGGAATTGC 59.349 37.037 17.07 0.00 40.44 3.56
1892 2768 2.651455 CTCCATGTGCTGGTCATTCAT 58.349 47.619 0.00 0.00 46.08 2.57
1911 2787 9.112725 TCATTCATTGGTAATCATCAAGTACTG 57.887 33.333 0.00 0.00 0.00 2.74
1912 2788 8.896744 CATTCATTGGTAATCATCAAGTACTGT 58.103 33.333 0.00 0.00 0.00 3.55
2208 3087 4.632538 ATTTTGCGTACTTATGGGAAGC 57.367 40.909 0.00 0.00 0.00 3.86
2287 3166 1.253593 CCTTTTCCCTGAAGGCTGCC 61.254 60.000 11.65 11.65 37.45 4.85
2641 3552 1.324736 GCTATAGCACGTGTCACTTGC 59.675 52.381 23.11 23.11 42.83 4.01
2872 3785 7.531857 TTCAGTGATCTATATCTCCTTGACC 57.468 40.000 0.00 0.00 32.93 4.02
3020 3933 2.749839 GGGCATGCAGGCGTAACA 60.750 61.111 21.36 0.00 45.36 2.41
3118 4031 2.736144 TACTGCGTCCATTCGTTTCT 57.264 45.000 0.00 0.00 0.00 2.52
3150 4063 5.163237 GGTAACCTAATGAATGTAGCTCCCA 60.163 44.000 0.00 0.00 0.00 4.37
3191 4104 9.974980 GTTATTCCACTTTGTTCCATTTCTAAA 57.025 29.630 0.00 0.00 0.00 1.85
3314 4227 0.165944 CTAGTTTTGAAGGCCGTGCG 59.834 55.000 0.00 0.00 0.00 5.34
3419 4333 5.924475 ATATGTTCCGCATAGTTACTTGC 57.076 39.130 8.67 8.67 42.68 4.01
3467 4382 2.552743 GGAGAAAGGGTCTTTTGGTTCG 59.447 50.000 0.00 0.00 36.41 3.95
3604 4519 4.333095 TGAGACTCATAGACTAAGCGTGAC 59.667 45.833 0.00 0.00 0.00 3.67
3633 4548 0.778815 CGAGTCGACACTGAAGTTGC 59.221 55.000 19.50 0.00 30.63 4.17
3636 4551 0.503117 GTCGACACTGAAGTTGCGAC 59.497 55.000 11.55 14.99 41.41 5.19
3841 4756 2.022195 TCTCCGTAATCTCCTTCACCG 58.978 52.381 0.00 0.00 0.00 4.94
3938 4853 1.073025 AGCAACGAGGCATGTTCCA 59.927 52.632 5.91 0.00 35.83 3.53
4042 4959 0.032130 TCTCAGACCAAGTGTGTCGC 59.968 55.000 0.00 0.00 37.80 5.19
4284 5204 3.369892 GCATGAGAAGAGCCAGGTAGAAA 60.370 47.826 0.00 0.00 0.00 2.52
4429 5349 4.039124 AATTCCATAATTTTGCCTAGGGCG 59.961 41.667 11.72 0.00 41.09 6.13
4459 5383 9.448438 TTGTGTGCTGAAGTTATCTGTAATATT 57.552 29.630 0.00 0.00 0.00 1.28
4558 5484 8.675705 TCAAACTCAAATCACTGTATCTCAAA 57.324 30.769 0.00 0.00 0.00 2.69
4591 5517 4.444720 GGTTGTCAGCGTAGTAGCATTATC 59.555 45.833 0.00 0.00 40.15 1.75
4600 5526 9.788960 CAGCGTAGTAGCATTATCTTTCATATA 57.211 33.333 0.00 0.00 40.15 0.86
4658 5589 4.515191 TCAGTTTATCAAACCTCACAGTGC 59.485 41.667 0.00 0.00 42.34 4.40
4887 5819 2.231235 GGTACGTAAAGGTTCTTCGGGA 59.769 50.000 0.00 0.00 0.00 5.14
4983 5931 5.654370 TGGGATAGGAGTGATGATGATACA 58.346 41.667 0.00 0.00 0.00 2.29
5091 6039 0.762418 TTGCTTCGGAGTGAAAGGGA 59.238 50.000 0.00 0.00 35.79 4.20
5363 6312 6.055588 CCAGAACCTCAGAAACTTGAAAGTA 58.944 40.000 0.00 0.00 38.57 2.24
5418 6367 0.031449 ATTTCCCGGCGTTGTTTGTG 59.969 50.000 6.01 0.00 0.00 3.33
5444 6393 5.064452 GTGTTTGAACATGGCATCACAAAAA 59.936 36.000 18.14 13.39 41.59 1.94
5462 6411 9.575868 TCACAAAAACATATTGGTAACTTAGGA 57.424 29.630 0.00 0.00 37.61 2.94
5500 6449 4.767928 AGCAGGTATTCTTCTATAGGGTCG 59.232 45.833 0.00 0.00 0.00 4.79
5501 6450 4.618693 GCAGGTATTCTTCTATAGGGTCGC 60.619 50.000 0.00 0.00 0.00 5.19
5630 6663 4.339872 AGCAAATCACAATCCAGCAAAA 57.660 36.364 0.00 0.00 0.00 2.44
5926 8234 4.573900 AGAAATCTTTGCAGTGATCGAGT 58.426 39.130 0.00 0.00 0.00 4.18
5992 8300 0.886490 GCCGCCATACAGGATTGAGG 60.886 60.000 0.00 0.00 41.22 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.318313 ACACGGGATAATCAGGATCCTT 58.682 45.455 13.00 0.00 42.32 3.36
217 623 2.139917 GATCACCTTGTACGTGCAACA 58.860 47.619 15.43 0.00 35.74 3.33
321 728 4.466370 TCTTACGTGAGATCACCTTTCCAT 59.534 41.667 5.85 0.00 43.66 3.41
325 732 4.283722 ACCTTCTTACGTGAGATCACCTTT 59.716 41.667 11.19 0.00 43.66 3.11
408 1226 7.027161 GGTAATAATTCTTGCGCTTTCTTTGA 58.973 34.615 9.73 0.00 0.00 2.69
439 1257 4.141779 ACTCCCCACTTCATCGGTTTATAC 60.142 45.833 0.00 0.00 0.00 1.47
440 1258 4.035112 ACTCCCCACTTCATCGGTTTATA 58.965 43.478 0.00 0.00 0.00 0.98
441 1259 2.844348 ACTCCCCACTTCATCGGTTTAT 59.156 45.455 0.00 0.00 0.00 1.40
480 1299 5.066764 CCCACCTTCGTTGTTTTCTTTTCTA 59.933 40.000 0.00 0.00 0.00 2.10
481 1300 4.142249 CCCACCTTCGTTGTTTTCTTTTCT 60.142 41.667 0.00 0.00 0.00 2.52
487 1306 1.003223 CGTCCCACCTTCGTTGTTTTC 60.003 52.381 0.00 0.00 0.00 2.29
491 1310 0.178533 TTTCGTCCCACCTTCGTTGT 59.821 50.000 0.00 0.00 0.00 3.32
494 1313 3.784642 TTTTTCGTCCCACCTTCGT 57.215 47.368 0.00 0.00 0.00 3.85
552 1373 8.103305 AGTCTCTATTTTTAATGGAGCAGTTGA 58.897 33.333 7.63 0.00 0.00 3.18
580 1401 5.710613 TGCCAACAATTTTCGTTTTTCTC 57.289 34.783 0.00 0.00 0.00 2.87
581 1402 5.872070 TCTTGCCAACAATTTTCGTTTTTCT 59.128 32.000 0.00 0.00 34.61 2.52
582 1403 6.100792 TCTTGCCAACAATTTTCGTTTTTC 57.899 33.333 0.00 0.00 34.61 2.29
583 1404 6.487689 TTCTTGCCAACAATTTTCGTTTTT 57.512 29.167 0.00 0.00 34.61 1.94
592 1413 4.992951 GCTCAGAATTTCTTGCCAACAATT 59.007 37.500 0.00 0.00 34.61 2.32
621 1442 0.725784 GGTCACTTCAAATGCGTGCG 60.726 55.000 0.00 0.00 0.00 5.34
645 1473 1.079057 GGAAGCTTCCTCCACGTCC 60.079 63.158 33.98 8.90 44.11 4.79
648 1476 1.446272 GACGGAAGCTTCCTCCACG 60.446 63.158 36.30 26.40 45.33 4.94
701 1536 2.298629 CGGTGCAGATCGATGCTCG 61.299 63.158 0.54 7.71 46.63 5.03
702 1537 0.319383 ATCGGTGCAGATCGATGCTC 60.319 55.000 15.69 3.29 43.97 4.26
703 1538 0.319383 GATCGGTGCAGATCGATGCT 60.319 55.000 19.70 0.00 45.67 3.79
704 1539 0.598419 TGATCGGTGCAGATCGATGC 60.598 55.000 19.70 2.63 45.67 3.91
705 1540 1.135046 GTGATCGGTGCAGATCGATG 58.865 55.000 19.70 0.00 45.67 3.84
709 1544 0.596083 CCTCGTGATCGGTGCAGATC 60.596 60.000 8.62 8.62 45.35 2.75
808 1643 1.682684 GGGAGAGGTTGCTCGGAGA 60.683 63.158 9.69 0.00 35.74 3.71
809 1644 2.726351 GGGGAGAGGTTGCTCGGAG 61.726 68.421 0.00 0.00 35.74 4.63
810 1645 2.683933 GGGGAGAGGTTGCTCGGA 60.684 66.667 0.00 0.00 35.74 4.55
811 1646 3.787001 GGGGGAGAGGTTGCTCGG 61.787 72.222 0.00 0.00 35.74 4.63
830 1674 1.110442 CAGAAGCCTCGAGATCTGGT 58.890 55.000 23.83 9.34 36.50 4.00
857 1711 3.157881 TCGAGATCTGGACAACACTCTT 58.842 45.455 0.00 0.00 0.00 2.85
985 1839 2.187685 CATCGCTGGCAGCAGGTA 59.812 61.111 35.94 19.78 42.58 3.08
998 1852 2.434884 AGCAACTCACCGGCATCG 60.435 61.111 0.00 0.00 0.00 3.84
1020 1874 2.543238 GCCCATGTGCTAGTACTACGAC 60.543 54.545 12.42 0.00 0.00 4.34
1022 1876 1.681793 AGCCCATGTGCTAGTACTACG 59.318 52.381 12.42 0.82 40.56 3.51
1026 1880 1.482593 ACTCAGCCCATGTGCTAGTAC 59.517 52.381 1.17 3.70 40.32 2.73
1033 1890 0.675837 CCACTCACTCAGCCCATGTG 60.676 60.000 0.00 0.00 0.00 3.21
1043 1900 0.952984 GAAGCCACAGCCACTCACTC 60.953 60.000 0.00 0.00 41.25 3.51
1132 1989 2.807967 CGATGTTTTTCTCCACTCAGCA 59.192 45.455 0.00 0.00 0.00 4.41
1133 1990 2.808543 ACGATGTTTTTCTCCACTCAGC 59.191 45.455 0.00 0.00 0.00 4.26
1136 1993 3.057734 ACGACGATGTTTTTCTCCACTC 58.942 45.455 0.00 0.00 0.00 3.51
1141 1998 4.846137 CCAATTCACGACGATGTTTTTCTC 59.154 41.667 0.00 0.00 0.00 2.87
1142 1999 4.274950 ACCAATTCACGACGATGTTTTTCT 59.725 37.500 0.00 0.00 0.00 2.52
1143 2000 4.533222 ACCAATTCACGACGATGTTTTTC 58.467 39.130 0.00 0.00 0.00 2.29
1144 2001 4.035792 TGACCAATTCACGACGATGTTTTT 59.964 37.500 0.00 0.00 0.00 1.94
1145 2002 3.562141 TGACCAATTCACGACGATGTTTT 59.438 39.130 0.00 0.00 0.00 2.43
1146 2003 3.135225 TGACCAATTCACGACGATGTTT 58.865 40.909 0.00 0.00 0.00 2.83
1147 2004 2.761559 TGACCAATTCACGACGATGTT 58.238 42.857 0.00 0.00 0.00 2.71
1148 2005 2.448926 TGACCAATTCACGACGATGT 57.551 45.000 0.00 0.00 0.00 3.06
1149 2006 2.929398 TCATGACCAATTCACGACGATG 59.071 45.455 0.00 0.00 36.92 3.84
1153 2014 3.325870 TCAGTCATGACCAATTCACGAC 58.674 45.455 22.21 0.00 45.97 4.34
1156 2017 6.017400 ACAAATCAGTCATGACCAATTCAC 57.983 37.500 22.21 0.00 38.57 3.18
1164 2030 8.119226 GCTAAGTCATTACAAATCAGTCATGAC 58.881 37.037 18.47 18.47 46.18 3.06
1184 2050 5.385198 TGAGAAGGAAAAACATGGCTAAGT 58.615 37.500 0.00 0.00 0.00 2.24
1187 2053 5.819991 AGATGAGAAGGAAAAACATGGCTA 58.180 37.500 0.00 0.00 0.00 3.93
1189 2055 5.166398 CAAGATGAGAAGGAAAAACATGGC 58.834 41.667 0.00 0.00 0.00 4.40
1214 2080 3.260632 TGCAGTGGTTCTTGTATGCTCTA 59.739 43.478 0.00 0.00 34.80 2.43
1348 2220 1.608717 GGACTGAGAGTGGCGTCCAT 61.609 60.000 1.90 0.00 44.11 3.41
1357 2229 0.902516 GCTGTCCTGGGACTGAGAGT 60.903 60.000 24.22 0.00 43.68 3.24
1427 2299 4.502259 CCAGCACAAGATCAGAGGGTATAC 60.502 50.000 0.00 0.00 0.00 1.47
1486 2361 4.320348 GCTCCATGCTGCAGAAGATAATTC 60.320 45.833 20.43 0.00 38.95 2.17
1676 2551 5.202004 TCTAGGGCTCAAGTAAAGGAGTAG 58.798 45.833 0.00 0.00 33.66 2.57
1687 2562 5.815233 TCTATGGAAATCTAGGGCTCAAG 57.185 43.478 0.00 0.00 0.00 3.02
1892 2768 8.458573 ACAAAACAGTACTTGATGATTACCAA 57.541 30.769 0.00 0.00 0.00 3.67
1931 2807 7.182060 ACCATTGGAATGTATACCAGTTTCTT 58.818 34.615 10.37 0.00 37.48 2.52
1932 2808 6.731467 ACCATTGGAATGTATACCAGTTTCT 58.269 36.000 10.37 0.00 37.48 2.52
1992 2869 3.307059 CCGGATGGAATCTACAGGGATTC 60.307 52.174 0.00 8.23 46.27 2.52
2238 3117 1.154225 GCGACCCAATTGAACAGCG 60.154 57.895 7.12 4.58 0.00 5.18
2872 3785 3.201290 ACAGAAGTCTCACTGTTTGCAG 58.799 45.455 6.78 0.00 43.52 4.41
3020 3933 4.790718 GATAACCCAGTTATCCCCAACT 57.209 45.455 13.99 0.00 44.84 3.16
3109 4022 5.944007 AGGTTACCAAATAGCAGAAACGAAT 59.056 36.000 3.51 0.00 0.00 3.34
3118 4031 9.337396 CTACATTCATTAGGTTACCAAATAGCA 57.663 33.333 3.51 0.00 0.00 3.49
3150 4063 8.380742 AGTGGAATAACCGATTATAGATGGAT 57.619 34.615 0.00 0.00 42.61 3.41
3210 4123 4.212847 GCATTAGGCACATGTGAGTGATAG 59.787 45.833 29.80 13.03 42.05 2.08
3314 4227 1.209747 CTAACCTCACTTGTAGGGGGC 59.790 57.143 0.00 0.00 38.54 5.80
3633 4548 5.234543 TCAGTGTCGATTAGTCTATGAGTCG 59.765 44.000 0.00 0.00 0.00 4.18
3636 4551 7.011950 AGACTTCAGTGTCGATTAGTCTATGAG 59.988 40.741 0.00 0.00 40.21 2.90
3711 4626 7.090808 TCACTATTACGCATGGATTATGAGTC 58.909 38.462 0.00 0.00 45.08 3.36
3841 4756 4.142227 TGAAGTACTAAACTCGATCCCTGC 60.142 45.833 0.00 0.00 37.50 4.85
3997 4914 7.389053 ACTTGTCTTCAGAGCATAAACCTAAAG 59.611 37.037 0.00 0.00 0.00 1.85
4042 4959 4.921547 TCGAGTTCATCTATTCGTGAAGG 58.078 43.478 0.00 0.00 35.22 3.46
4175 5092 0.232816 CGTTAACCGTGGTTCCAACG 59.767 55.000 19.48 19.48 40.85 4.10
4429 5349 5.696724 ACAGATAACTTCAGCACACAAGTAC 59.303 40.000 0.00 0.00 32.36 2.73
4510 5436 0.905357 TCTGAAGCTCAGGGCCTTAC 59.095 55.000 1.32 0.00 44.39 2.34
4558 5484 4.755266 ACGCTGACAACCTATAATTCCT 57.245 40.909 0.00 0.00 0.00 3.36
4600 5526 7.707624 TTGAGACTCCAATTCAAGCATAAAT 57.292 32.000 0.00 0.00 0.00 1.40
4658 5589 7.482654 TCTCTCTCTGTGTGTAAATGTTTTG 57.517 36.000 0.00 0.00 0.00 2.44
4983 5931 3.494223 CCAATTCGGCAAAGGGAAAACTT 60.494 43.478 0.00 0.00 0.00 2.66
5091 6039 0.327924 TGATTTGTCAGACCCGCCAT 59.672 50.000 0.00 0.00 0.00 4.40
5389 6338 2.696707 ACGCCGGGAAATATTACTCAGA 59.303 45.455 2.18 0.00 0.00 3.27
5390 6339 3.107642 ACGCCGGGAAATATTACTCAG 57.892 47.619 2.18 0.00 0.00 3.35
5396 6345 2.559231 ACAAACAACGCCGGGAAATATT 59.441 40.909 2.18 0.00 0.00 1.28
5406 6355 1.388431 CAAACACACACAAACAACGCC 59.612 47.619 0.00 0.00 0.00 5.68
5418 6367 3.052036 GTGATGCCATGTTCAAACACAC 58.948 45.455 0.00 0.00 42.51 3.82
5500 6449 3.368495 ACGACCAAAAATGAAAGAACGC 58.632 40.909 0.00 0.00 0.00 4.84
5501 6450 5.741982 AGAAACGACCAAAAATGAAAGAACG 59.258 36.000 0.00 0.00 0.00 3.95
5739 6777 7.280044 AGGGTAATACCTGAAGTTACCAATT 57.720 36.000 9.58 0.00 45.80 2.32
5752 6790 5.826643 TGAAAAATCTGCAGGGTAATACCT 58.173 37.500 15.13 0.00 43.08 3.08
5759 6797 4.039124 ACGAATTTGAAAAATCTGCAGGGT 59.961 37.500 15.13 0.00 0.00 4.34
5797 6835 8.275040 AGCTTCCTTCTGTATTATGGTTATGTT 58.725 33.333 0.00 0.00 0.00 2.71
5926 8234 9.409312 CATGTGATATGTTTGTTTTCAAGCTTA 57.591 29.630 0.00 0.00 40.75 3.09
5992 8300 3.898482 ACTATTAATGTGAACCTGGCCC 58.102 45.455 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.