Multiple sequence alignment - TraesCS5A01G327600

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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 TraesCS5A01G327600 chr5A 100.000 3017 0 0 1 3017 537119257 537116241 0.000000e+00 5572.0
1 TraesCS5A01G327600 chr5A 97.140 944 26 1 2075 3017 680908918 680907975 0.000000e+00 1592.0
2 TraesCS5A01G327600 chr5A 85.729 995 125 16 1053 2035 537249038 537250027 0.000000e+00 1035.0
3 TraesCS5A01G327600 chr5B 92.616 1598 62 24 504 2074 511362571 511361003 0.000000e+00 2246.0
4 TraesCS5A01G327600 chr5B 84.940 996 130 18 1053 2035 511602151 511603139 0.000000e+00 990.0
5 TraesCS5A01G327600 chr5B 89.077 531 49 7 2074 2602 115365894 115365371 0.000000e+00 651.0
6 TraesCS5A01G327600 chr5B 84.186 430 47 16 78 504 511363015 511362604 6.060000e-107 398.0
7 TraesCS5A01G327600 chr5D 90.128 1489 95 33 601 2074 423513312 423511861 0.000000e+00 1888.0
8 TraesCS5A01G327600 chr5D 84.662 991 132 17 1053 2030 423756765 423757748 0.000000e+00 970.0
9 TraesCS5A01G327600 chr3A 93.319 943 56 7 2076 3016 73608291 73607354 0.000000e+00 1386.0
10 TraesCS5A01G327600 chr1A 92.381 945 63 7 2074 3016 586941796 586940859 0.000000e+00 1338.0
11 TraesCS5A01G327600 chr4A 92.694 917 62 5 2075 2989 546616038 546615125 0.000000e+00 1317.0
12 TraesCS5A01G327600 chr4A 90.651 952 76 9 2071 3017 611281864 611282807 0.000000e+00 1253.0
13 TraesCS5A01G327600 chr7B 90.075 534 43 8 2072 2602 610093074 610093600 0.000000e+00 684.0
14 TraesCS5A01G327600 chr1D 90.189 530 44 8 2075 2602 30658447 30657924 0.000000e+00 684.0
15 TraesCS5A01G327600 chr4B 88.722 532 52 7 2075 2604 133917742 133917217 0.000000e+00 643.0
16 TraesCS5A01G327600 chr3B 82.184 174 14 8 2835 3006 761198336 761198178 1.890000e-27 134.0
17 TraesCS5A01G327600 chr2A 100.000 29 0 0 1230 1258 49068505 49068477 2.000000e-03 54.7


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 TraesCS5A01G327600 chr5A 537116241 537119257 3016 True 5572 5572 100.000 1 3017 1 chr5A.!!$R1 3016
1 TraesCS5A01G327600 chr5A 680907975 680908918 943 True 1592 1592 97.140 2075 3017 1 chr5A.!!$R2 942
2 TraesCS5A01G327600 chr5A 537249038 537250027 989 False 1035 1035 85.729 1053 2035 1 chr5A.!!$F1 982
3 TraesCS5A01G327600 chr5B 511361003 511363015 2012 True 1322 2246 88.401 78 2074 2 chr5B.!!$R2 1996
4 TraesCS5A01G327600 chr5B 511602151 511603139 988 False 990 990 84.940 1053 2035 1 chr5B.!!$F1 982
5 TraesCS5A01G327600 chr5B 115365371 115365894 523 True 651 651 89.077 2074 2602 1 chr5B.!!$R1 528
6 TraesCS5A01G327600 chr5D 423511861 423513312 1451 True 1888 1888 90.128 601 2074 1 chr5D.!!$R1 1473
7 TraesCS5A01G327600 chr5D 423756765 423757748 983 False 970 970 84.662 1053 2030 1 chr5D.!!$F1 977
8 TraesCS5A01G327600 chr3A 73607354 73608291 937 True 1386 1386 93.319 2076 3016 1 chr3A.!!$R1 940
9 TraesCS5A01G327600 chr1A 586940859 586941796 937 True 1338 1338 92.381 2074 3016 1 chr1A.!!$R1 942
10 TraesCS5A01G327600 chr4A 546615125 546616038 913 True 1317 1317 92.694 2075 2989 1 chr4A.!!$R1 914
11 TraesCS5A01G327600 chr4A 611281864 611282807 943 False 1253 1253 90.651 2071 3017 1 chr4A.!!$F1 946
12 TraesCS5A01G327600 chr7B 610093074 610093600 526 False 684 684 90.075 2072 2602 1 chr7B.!!$F1 530
13 TraesCS5A01G327600 chr1D 30657924 30658447 523 True 684 684 90.189 2075 2602 1 chr1D.!!$R1 527
14 TraesCS5A01G327600 chr4B 133917217 133917742 525 True 643 643 88.722 2075 2604 1 chr4B.!!$R1 529

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
450 469 0.103937 CTGTCTCTCTGCCGGGATTC 59.896 60.0 2.18 0.0 0.0 2.52 F
474 493 0.679505 TGCTATCGTACCATCCCTGC 59.320 55.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1874 0.033699 GTACAGGTACCTCCGGTCCT 60.034 60.000 12.84 0.08 43.2 3.85 R
2319 2424 1.138883 GCATGACTACGGACGCTCA 59.861 57.895 0.00 0.00 0.0 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
20 21 3.075866 GCATGGTCAGCTAAATTGCTC 57.924 47.619 0.00 0.00 41.98 4.26
21 22 2.540361 GCATGGTCAGCTAAATTGCTCG 60.540 50.000 0.00 0.00 41.98 5.03
22 23 2.760634 TGGTCAGCTAAATTGCTCGA 57.239 45.000 0.00 0.00 41.98 4.04
23 24 3.052455 TGGTCAGCTAAATTGCTCGAA 57.948 42.857 0.00 0.00 41.98 3.71
24 25 3.002791 TGGTCAGCTAAATTGCTCGAAG 58.997 45.455 0.00 0.00 41.98 3.79
25 26 2.223135 GGTCAGCTAAATTGCTCGAAGC 60.223 50.000 0.00 0.00 41.98 3.86
36 37 2.876992 GCTCGAAGCATGCATGATAG 57.123 50.000 30.64 20.50 41.89 2.08
37 38 1.463831 GCTCGAAGCATGCATGATAGG 59.536 52.381 30.64 18.47 41.89 2.57
38 39 2.869237 GCTCGAAGCATGCATGATAGGA 60.869 50.000 30.64 21.43 41.89 2.94
39 40 3.597255 CTCGAAGCATGCATGATAGGAT 58.403 45.455 30.64 8.91 0.00 3.24
40 41 3.332034 TCGAAGCATGCATGATAGGATG 58.668 45.455 30.64 12.37 39.94 3.51
41 42 3.007182 TCGAAGCATGCATGATAGGATGA 59.993 43.478 30.64 14.39 39.40 2.92
42 43 3.371285 CGAAGCATGCATGATAGGATGAG 59.629 47.826 30.64 7.25 39.40 2.90
43 44 3.351794 AGCATGCATGATAGGATGAGG 57.648 47.619 30.64 0.00 39.40 3.86
44 45 1.743958 GCATGCATGATAGGATGAGGC 59.256 52.381 30.64 6.16 39.40 4.70
45 46 2.366533 CATGCATGATAGGATGAGGCC 58.633 52.381 22.59 0.00 39.40 5.19
46 47 1.437397 TGCATGATAGGATGAGGCCA 58.563 50.000 5.01 0.00 0.00 5.36
47 48 1.990327 TGCATGATAGGATGAGGCCAT 59.010 47.619 5.01 0.00 35.29 4.40
48 49 2.026542 TGCATGATAGGATGAGGCCATC 60.027 50.000 5.01 0.00 46.50 3.51
61 62 3.274586 CCATCATGTGGCTCGCCG 61.275 66.667 3.14 0.00 42.12 6.46
62 63 2.512286 CATCATGTGGCTCGCCGT 60.512 61.111 3.14 0.00 39.42 5.68
63 64 2.512286 ATCATGTGGCTCGCCGTG 60.512 61.111 3.14 2.80 39.42 4.94
64 65 3.315142 ATCATGTGGCTCGCCGTGT 62.315 57.895 3.14 0.00 39.42 4.49
65 66 3.792047 CATGTGGCTCGCCGTGTG 61.792 66.667 3.14 0.00 39.42 3.82
66 67 4.314440 ATGTGGCTCGCCGTGTGT 62.314 61.111 3.14 0.00 39.42 3.72
67 68 3.825160 ATGTGGCTCGCCGTGTGTT 62.825 57.895 3.14 0.00 39.42 3.32
68 69 4.012895 GTGGCTCGCCGTGTGTTG 62.013 66.667 3.14 0.00 39.42 3.33
71 72 4.374702 GCTCGCCGTGTGTTGCAG 62.375 66.667 0.00 0.00 0.00 4.41
72 73 4.374702 CTCGCCGTGTGTTGCAGC 62.375 66.667 0.00 0.00 0.00 5.25
126 127 2.101582 GCTACTGATTGGTCTCATCCGT 59.898 50.000 0.00 0.00 0.00 4.69
150 151 9.887406 CGTTTTATTACTGTACAAAAATGGAGT 57.113 29.630 11.57 1.11 0.00 3.85
174 175 0.969149 ACAGAGCTCGTGGTTCATGA 59.031 50.000 8.37 0.00 0.00 3.07
222 223 2.968697 GCCCGTTCGTGTCCGTTT 60.969 61.111 0.00 0.00 35.01 3.60
229 230 3.472431 CGTTCGTGTCCGTTTATTTTCC 58.528 45.455 0.00 0.00 35.01 3.13
231 232 4.318974 CGTTCGTGTCCGTTTATTTTCCTT 60.319 41.667 0.00 0.00 35.01 3.36
261 262 6.071165 AGGGGAATTTCTGAATGCTAAAACTG 60.071 38.462 0.00 0.00 0.00 3.16
266 267 9.415544 GAATTTCTGAATGCTAAAACTGTTCAT 57.584 29.630 0.00 0.00 0.00 2.57
273 274 2.595386 CTAAAACTGTTCATTGGCGCC 58.405 47.619 22.73 22.73 0.00 6.53
287 288 2.646175 GCGCCAGTCACCTACAGGA 61.646 63.158 1.29 0.00 36.90 3.86
288 289 1.215647 CGCCAGTCACCTACAGGAC 59.784 63.158 1.29 0.00 36.90 3.85
289 290 1.532604 CGCCAGTCACCTACAGGACA 61.533 60.000 1.29 0.00 36.90 4.02
290 291 0.685097 GCCAGTCACCTACAGGACAA 59.315 55.000 1.29 0.00 36.90 3.18
291 292 1.071699 GCCAGTCACCTACAGGACAAA 59.928 52.381 1.29 0.00 36.90 2.83
306 307 4.157289 CAGGACAAATTCACTCATTCTGGG 59.843 45.833 0.00 0.00 0.00 4.45
350 351 6.183360 CGTCGTAACTGTTGAATATTCCGAAA 60.183 38.462 12.90 0.00 0.00 3.46
351 352 7.512297 GTCGTAACTGTTGAATATTCCGAAAA 58.488 34.615 12.90 0.00 0.00 2.29
352 353 8.011106 GTCGTAACTGTTGAATATTCCGAAAAA 58.989 33.333 12.90 0.00 0.00 1.94
383 384 7.184067 ACTATTGAGTAGTTCCGAATTTCCT 57.816 36.000 0.00 0.00 40.80 3.36
389 390 5.544650 AGTAGTTCCGAATTTCCTTTTCGA 58.455 37.500 7.34 0.00 46.73 3.71
393 394 5.240844 AGTTCCGAATTTCCTTTTCGAATGT 59.759 36.000 0.00 0.00 46.73 2.71
421 422 5.791336 TGGATATACGAGTTGAGATGCTT 57.209 39.130 0.00 0.00 0.00 3.91
423 424 5.985530 TGGATATACGAGTTGAGATGCTTTG 59.014 40.000 0.00 0.00 0.00 2.77
448 467 1.760086 CCTGTCTCTCTGCCGGGAT 60.760 63.158 2.18 0.00 0.00 3.85
449 468 1.333636 CCTGTCTCTCTGCCGGGATT 61.334 60.000 2.18 0.00 0.00 3.01
450 469 0.103937 CTGTCTCTCTGCCGGGATTC 59.896 60.000 2.18 0.00 0.00 2.52
459 478 1.148273 GCCGGGATTCCACATGCTA 59.852 57.895 2.18 0.00 0.00 3.49
470 489 2.299013 TCCACATGCTATCGTACCATCC 59.701 50.000 0.00 0.00 0.00 3.51
473 492 2.300152 ACATGCTATCGTACCATCCCTG 59.700 50.000 0.00 0.00 0.00 4.45
474 493 0.679505 TGCTATCGTACCATCCCTGC 59.320 55.000 0.00 0.00 0.00 4.85
485 504 1.075748 ATCCCTGCCCTGCAAATCC 60.076 57.895 0.00 0.00 38.41 3.01
491 510 1.980772 GCCCTGCAAATCCACTGCT 60.981 57.895 0.00 0.00 40.59 4.24
510 562 2.607635 GCTTAAATCCGAATCACGAGCA 59.392 45.455 0.00 0.00 45.77 4.26
531 583 4.726416 CATTTCGTCCCAAAGTCTTCATG 58.274 43.478 0.00 0.00 0.00 3.07
538 590 3.117701 TCCCAAAGTCTTCATGGACACAA 60.118 43.478 5.05 0.00 38.57 3.33
540 592 3.885297 CCAAAGTCTTCATGGACACAACT 59.115 43.478 5.12 0.00 38.57 3.16
552 604 7.619965 TCATGGACACAACTGAATTATACAGA 58.380 34.615 0.00 0.00 38.55 3.41
565 617 5.537300 ATTATACAGACACGAGCTCCATT 57.463 39.130 8.47 0.00 0.00 3.16
692 747 0.748005 ATATTGTCCGTGCTGCCACC 60.748 55.000 0.00 0.00 38.79 4.61
778 840 1.303091 AATAACACGCCACGCTTCCC 61.303 55.000 0.00 0.00 0.00 3.97
797 859 1.687493 CCCTCGCTTCCTCCTCCTT 60.687 63.158 0.00 0.00 0.00 3.36
804 867 1.695989 GCTTCCTCCTCCTTCCCCATA 60.696 57.143 0.00 0.00 0.00 2.74
808 871 1.062121 CCTCCTCCTTCCCCATAGACA 60.062 57.143 0.00 0.00 0.00 3.41
880 973 4.669206 TTTGGCGCCATTAATCAATCAT 57.331 36.364 33.25 0.00 0.00 2.45
882 975 3.220940 TGGCGCCATTAATCAATCATCA 58.779 40.909 29.03 0.00 0.00 3.07
908 1001 2.123897 GCCCCGAGCTCTCTCTCT 60.124 66.667 12.85 0.00 38.99 3.10
909 1002 2.193536 GCCCCGAGCTCTCTCTCTC 61.194 68.421 12.85 0.00 38.99 3.20
912 1005 4.124910 CGAGCTCTCTCTCTCGCT 57.875 61.111 12.85 0.00 44.30 4.93
913 1006 1.934463 CGAGCTCTCTCTCTCGCTC 59.066 63.158 12.85 0.00 44.30 5.03
990 1083 5.152934 AGCCGTTATTTATAGGAAGGAGGA 58.847 41.667 0.00 0.00 0.00 3.71
991 1084 5.246429 AGCCGTTATTTATAGGAAGGAGGAG 59.754 44.000 0.00 0.00 0.00 3.69
992 1085 5.569026 GCCGTTATTTATAGGAAGGAGGAGG 60.569 48.000 0.00 0.00 0.00 4.30
1045 1138 3.044305 ACGACAGCGGCAAGAAGC 61.044 61.111 1.45 0.00 43.17 3.86
1446 1542 2.202324 GTGCTCGACGACGTCCTC 60.202 66.667 21.63 7.25 40.69 3.71
1449 1545 2.812609 CTCGACGACGTCCTCCGA 60.813 66.667 21.63 14.80 40.70 4.55
1587 1683 2.030562 CAGGACGAGGCGGTGTTT 59.969 61.111 0.00 0.00 0.00 2.83
1589 1685 2.029964 GGACGAGGCGGTGTTTCA 59.970 61.111 0.00 0.00 0.00 2.69
2083 2183 1.774085 CGCGCGATTAGTGTTAGAGTC 59.226 52.381 28.94 0.00 0.00 3.36
2086 2186 3.544834 GCGCGATTAGTGTTAGAGTCGTA 60.545 47.826 12.10 0.00 0.00 3.43
2135 2235 5.670792 ATAGTTGGATTTGGAGTCGTACA 57.329 39.130 0.00 0.00 0.00 2.90
2311 2416 1.591158 GTGCGGTATTGTGACGGTATG 59.409 52.381 0.00 0.00 0.00 2.39
2319 2424 1.801242 TGTGACGGTATGATGGGGAT 58.199 50.000 0.00 0.00 0.00 3.85
2325 2430 0.687354 GGTATGATGGGGATGAGCGT 59.313 55.000 0.00 0.00 0.00 5.07
2365 2470 3.466836 GATGTAGCCATGATCGGTGAAA 58.533 45.455 0.00 0.00 0.00 2.69
2576 2684 2.203788 AGGAGGACCTCGGCAACA 60.204 61.111 15.46 0.00 44.13 3.33
2774 2882 0.670546 CTTGCCAGGGTGTGTACGAG 60.671 60.000 0.00 0.00 0.00 4.18
2945 3053 2.753966 GCCGCGTGATGCAAGACAT 61.754 57.895 4.92 0.00 46.97 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.540361 CGAGCAATTTAGCTGACCATGC 60.540 50.000 0.00 0.47 46.75 4.06
1 2 2.938451 TCGAGCAATTTAGCTGACCATG 59.062 45.455 0.00 0.00 46.75 3.66
2 3 3.266510 TCGAGCAATTTAGCTGACCAT 57.733 42.857 0.00 0.00 46.75 3.55
3 4 2.760634 TCGAGCAATTTAGCTGACCA 57.239 45.000 0.00 0.00 46.75 4.02
4 5 2.223135 GCTTCGAGCAATTTAGCTGACC 60.223 50.000 0.00 0.00 46.75 4.02
5 6 3.044959 GCTTCGAGCAATTTAGCTGAC 57.955 47.619 0.00 0.00 46.75 3.51
17 18 1.463831 CCTATCATGCATGCTTCGAGC 59.536 52.381 22.25 0.58 42.82 5.03
18 19 3.036075 TCCTATCATGCATGCTTCGAG 57.964 47.619 22.25 12.68 0.00 4.04
19 20 3.007182 TCATCCTATCATGCATGCTTCGA 59.993 43.478 22.25 14.10 0.00 3.71
20 21 3.332034 TCATCCTATCATGCATGCTTCG 58.668 45.455 22.25 9.28 0.00 3.79
21 22 3.690139 CCTCATCCTATCATGCATGCTTC 59.310 47.826 22.25 0.00 0.00 3.86
22 23 3.687125 CCTCATCCTATCATGCATGCTT 58.313 45.455 22.25 10.16 0.00 3.91
23 24 2.618302 GCCTCATCCTATCATGCATGCT 60.618 50.000 22.25 15.24 0.00 3.79
24 25 1.743958 GCCTCATCCTATCATGCATGC 59.256 52.381 22.25 11.82 0.00 4.06
25 26 2.290705 TGGCCTCATCCTATCATGCATG 60.291 50.000 21.07 21.07 0.00 4.06
26 27 1.990327 TGGCCTCATCCTATCATGCAT 59.010 47.619 3.32 0.00 0.00 3.96
27 28 1.437397 TGGCCTCATCCTATCATGCA 58.563 50.000 3.32 0.00 0.00 3.96
28 29 2.026542 TGATGGCCTCATCCTATCATGC 60.027 50.000 3.32 0.00 46.92 4.06
29 30 3.994931 TGATGGCCTCATCCTATCATG 57.005 47.619 3.32 0.00 46.92 3.07
30 31 3.850774 ACATGATGGCCTCATCCTATCAT 59.149 43.478 12.98 9.91 46.92 2.45
31 32 3.008704 CACATGATGGCCTCATCCTATCA 59.991 47.826 12.98 8.15 46.92 2.15
32 33 3.607741 CACATGATGGCCTCATCCTATC 58.392 50.000 12.98 2.88 46.92 2.08
33 34 2.307980 CCACATGATGGCCTCATCCTAT 59.692 50.000 12.98 0.00 46.92 2.57
34 35 1.701292 CCACATGATGGCCTCATCCTA 59.299 52.381 12.98 0.00 46.92 2.94
35 36 0.477204 CCACATGATGGCCTCATCCT 59.523 55.000 12.98 0.00 46.92 3.24
36 37 3.031916 CCACATGATGGCCTCATCC 57.968 57.895 12.98 0.00 46.92 3.51
45 46 2.512286 ACGGCGAGCCACATGATG 60.512 61.111 16.62 0.00 35.37 3.07
46 47 2.512286 CACGGCGAGCCACATGAT 60.512 61.111 16.62 0.00 35.37 2.45
47 48 4.002506 ACACGGCGAGCCACATGA 62.003 61.111 16.62 0.00 35.37 3.07
48 49 3.792047 CACACGGCGAGCCACATG 61.792 66.667 16.62 11.07 35.37 3.21
49 50 3.825160 AACACACGGCGAGCCACAT 62.825 57.895 16.62 0.00 35.37 3.21
50 51 4.539083 AACACACGGCGAGCCACA 62.539 61.111 16.62 0.00 35.37 4.17
51 52 4.012895 CAACACACGGCGAGCCAC 62.013 66.667 16.62 0.00 35.37 5.01
54 55 4.374702 CTGCAACACACGGCGAGC 62.375 66.667 16.62 8.03 0.00 5.03
55 56 4.374702 GCTGCAACACACGGCGAG 62.375 66.667 16.62 8.85 0.00 5.03
60 61 4.707840 CTCGCGCTGCAACACACG 62.708 66.667 5.56 0.00 0.00 4.49
65 66 4.030452 AAAGGCTCGCGCTGCAAC 62.030 61.111 21.46 8.59 36.09 4.17
66 67 4.029186 CAAAGGCTCGCGCTGCAA 62.029 61.111 21.46 0.00 36.09 4.08
144 145 3.997021 CACGAGCTCTGTTTTTACTCCAT 59.003 43.478 12.85 0.00 0.00 3.41
150 151 3.799366 TGAACCACGAGCTCTGTTTTTA 58.201 40.909 12.85 2.11 0.00 1.52
151 152 2.639065 TGAACCACGAGCTCTGTTTTT 58.361 42.857 12.85 6.69 0.00 1.94
174 175 2.167219 CGTGCGATCGCTGTCCAAT 61.167 57.895 37.01 0.00 42.51 3.16
229 230 5.727434 CATTCAGAAATTCCCCTCCAAAAG 58.273 41.667 0.00 0.00 0.00 2.27
231 232 3.515104 GCATTCAGAAATTCCCCTCCAAA 59.485 43.478 0.00 0.00 0.00 3.28
247 248 5.229423 GCCAATGAACAGTTTTAGCATTCA 58.771 37.500 0.00 0.00 34.03 2.57
261 262 1.210155 GTGACTGGCGCCAATGAAC 59.790 57.895 32.09 21.27 0.00 3.18
273 274 4.452455 GTGAATTTGTCCTGTAGGTGACTG 59.548 45.833 0.00 0.00 43.88 3.51
287 288 2.827921 GGCCCAGAATGAGTGAATTTGT 59.172 45.455 0.00 0.00 39.69 2.83
288 289 2.159338 CGGCCCAGAATGAGTGAATTTG 60.159 50.000 0.00 0.00 39.69 2.32
289 290 2.094675 CGGCCCAGAATGAGTGAATTT 58.905 47.619 0.00 0.00 39.69 1.82
290 291 1.004745 ACGGCCCAGAATGAGTGAATT 59.995 47.619 0.00 0.00 39.69 2.17
291 292 0.620556 ACGGCCCAGAATGAGTGAAT 59.379 50.000 0.00 0.00 39.69 2.57
358 359 8.302515 AGGAAATTCGGAACTACTCAATAGTA 57.697 34.615 0.00 0.00 43.79 1.82
359 360 7.184067 AGGAAATTCGGAACTACTCAATAGT 57.816 36.000 0.00 0.00 46.75 2.12
360 361 8.494016 AAAGGAAATTCGGAACTACTCAATAG 57.506 34.615 0.00 0.00 36.89 1.73
361 362 8.857694 AAAAGGAAATTCGGAACTACTCAATA 57.142 30.769 0.00 0.00 0.00 1.90
362 363 7.360946 CGAAAAGGAAATTCGGAACTACTCAAT 60.361 37.037 0.00 0.00 44.36 2.57
363 364 6.073440 CGAAAAGGAAATTCGGAACTACTCAA 60.073 38.462 0.00 0.00 44.36 3.02
364 365 5.407387 CGAAAAGGAAATTCGGAACTACTCA 59.593 40.000 0.00 0.00 44.36 3.41
365 366 5.855235 CGAAAAGGAAATTCGGAACTACTC 58.145 41.667 0.00 0.00 44.36 2.59
366 367 5.857822 CGAAAAGGAAATTCGGAACTACT 57.142 39.130 0.00 0.00 44.36 2.57
375 376 8.647226 CCAACATAACATTCGAAAAGGAAATTC 58.353 33.333 0.00 0.00 0.00 2.17
376 377 8.364142 TCCAACATAACATTCGAAAAGGAAATT 58.636 29.630 0.00 0.00 0.00 1.82
377 378 7.891561 TCCAACATAACATTCGAAAAGGAAAT 58.108 30.769 0.00 0.00 0.00 2.17
378 379 7.278461 TCCAACATAACATTCGAAAAGGAAA 57.722 32.000 0.00 0.00 0.00 3.13
379 380 6.885952 TCCAACATAACATTCGAAAAGGAA 57.114 33.333 0.00 0.00 0.00 3.36
380 381 8.746052 ATATCCAACATAACATTCGAAAAGGA 57.254 30.769 0.00 0.00 0.00 3.36
381 382 9.878599 GTATATCCAACATAACATTCGAAAAGG 57.121 33.333 0.00 0.00 0.00 3.11
382 383 9.580916 CGTATATCCAACATAACATTCGAAAAG 57.419 33.333 0.00 0.00 0.00 2.27
383 384 9.315525 TCGTATATCCAACATAACATTCGAAAA 57.684 29.630 0.00 0.00 0.00 2.29
389 390 9.261180 CTCAACTCGTATATCCAACATAACATT 57.739 33.333 0.00 0.00 0.00 2.71
393 394 7.598869 GCATCTCAACTCGTATATCCAACATAA 59.401 37.037 0.00 0.00 0.00 1.90
448 467 3.244078 GGATGGTACGATAGCATGTGGAA 60.244 47.826 12.33 0.00 45.96 3.53
449 468 2.299013 GGATGGTACGATAGCATGTGGA 59.701 50.000 12.33 0.00 45.96 4.02
450 469 2.612972 GGGATGGTACGATAGCATGTGG 60.613 54.545 12.33 0.00 45.96 4.17
459 478 1.074471 AGGGCAGGGATGGTACGAT 60.074 57.895 0.00 0.00 0.00 3.73
470 489 1.304713 AGTGGATTTGCAGGGCAGG 60.305 57.895 0.00 0.00 40.61 4.85
473 492 1.538687 AAGCAGTGGATTTGCAGGGC 61.539 55.000 0.00 0.00 43.92 5.19
474 493 1.838112 TAAGCAGTGGATTTGCAGGG 58.162 50.000 0.00 0.00 43.92 4.45
485 504 3.616821 TCGTGATTCGGATTTAAGCAGTG 59.383 43.478 0.00 0.00 40.32 3.66
491 510 5.501736 CGAAATGCTCGTGATTCGGATTTAA 60.502 40.000 10.59 0.00 42.89 1.52
510 562 3.758554 CCATGAAGACTTTGGGACGAAAT 59.241 43.478 0.00 0.00 0.00 2.17
531 583 6.183360 CGTGTCTGTATAATTCAGTTGTGTCC 60.183 42.308 0.00 0.00 34.86 4.02
538 590 5.450688 GGAGCTCGTGTCTGTATAATTCAGT 60.451 44.000 7.83 0.00 34.86 3.41
540 592 4.401202 TGGAGCTCGTGTCTGTATAATTCA 59.599 41.667 7.83 0.00 0.00 2.57
587 641 4.362470 TGCAGCTTATCAATATGGAGCT 57.638 40.909 0.00 0.00 43.96 4.09
591 645 6.183360 CGATAGGTTGCAGCTTATCAATATGG 60.183 42.308 25.17 9.83 0.00 2.74
699 754 2.761160 GTTAGGTGGGTGGGTGGG 59.239 66.667 0.00 0.00 0.00 4.61
778 840 3.157949 GGAGGAGGAAGCGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
781 843 1.681486 GGGAAGGAGGAGGAAGCGAG 61.681 65.000 0.00 0.00 0.00 5.03
782 844 1.686110 GGGAAGGAGGAGGAAGCGA 60.686 63.158 0.00 0.00 0.00 4.93
783 845 2.736826 GGGGAAGGAGGAGGAAGCG 61.737 68.421 0.00 0.00 0.00 4.68
784 846 0.990818 ATGGGGAAGGAGGAGGAAGC 60.991 60.000 0.00 0.00 0.00 3.86
785 847 2.090494 TCTATGGGGAAGGAGGAGGAAG 60.090 54.545 0.00 0.00 0.00 3.46
786 848 1.944588 TCTATGGGGAAGGAGGAGGAA 59.055 52.381 0.00 0.00 0.00 3.36
787 849 1.220750 GTCTATGGGGAAGGAGGAGGA 59.779 57.143 0.00 0.00 0.00 3.71
797 859 2.771943 GTGGAGATGTTGTCTATGGGGA 59.228 50.000 0.00 0.00 37.29 4.81
804 867 2.639347 TGGACATGTGGAGATGTTGTCT 59.361 45.455 1.15 0.00 36.67 3.41
808 871 4.842531 TGTATGGACATGTGGAGATGTT 57.157 40.909 1.15 0.00 36.67 2.71
880 973 2.525629 TCGGGGCTGGTTGACTGA 60.526 61.111 0.00 0.00 0.00 3.41
882 975 4.021925 GCTCGGGGCTGGTTGACT 62.022 66.667 0.00 0.00 38.06 3.41
902 995 2.184579 TCGAGCGAGCGAGAGAGA 59.815 61.111 0.00 0.00 35.01 3.10
945 1038 2.923035 CCTGGACCTGGACGTGGT 60.923 66.667 12.01 0.00 41.07 4.16
947 1040 2.159819 CTGACCTGGACCTGGACGTG 62.160 65.000 23.36 10.50 0.00 4.49
948 1041 1.908793 CTGACCTGGACCTGGACGT 60.909 63.158 23.36 1.40 0.00 4.34
949 1042 1.599606 CTCTGACCTGGACCTGGACG 61.600 65.000 23.36 13.09 0.00 4.79
950 1043 1.893919 GCTCTGACCTGGACCTGGAC 61.894 65.000 23.36 17.39 0.00 4.02
951 1044 1.610673 GCTCTGACCTGGACCTGGA 60.611 63.158 23.36 1.59 0.00 3.86
953 1046 2.985456 GGCTCTGACCTGGACCTG 59.015 66.667 0.00 0.00 0.00 4.00
954 1047 2.681778 CGGCTCTGACCTGGACCT 60.682 66.667 0.00 0.00 0.00 3.85
955 1048 1.255667 TAACGGCTCTGACCTGGACC 61.256 60.000 0.00 0.00 0.00 4.46
990 1083 4.115199 GAAGACATGGCCGGCCCT 62.115 66.667 41.75 31.08 34.56 5.19
992 1085 4.115199 AGGAAGACATGGCCGGCC 62.115 66.667 39.40 39.40 0.00 6.13
1443 1539 0.752009 TCTCGGACAGGAATCGGAGG 60.752 60.000 9.59 0.00 43.03 4.30
1446 1542 1.437986 GGTCTCGGACAGGAATCGG 59.562 63.158 6.41 0.00 33.68 4.18
1449 1545 0.898789 ACACGGTCTCGGACAGGAAT 60.899 55.000 8.48 0.00 41.39 3.01
1587 1683 3.263503 CTCCGCGACCGTCTTGTGA 62.264 63.158 8.23 0.00 0.00 3.58
1589 1685 4.719369 GCTCCGCGACCGTCTTGT 62.719 66.667 8.23 0.00 0.00 3.16
1695 1791 0.608130 TGTCGATCCAGTTGTCCCTG 59.392 55.000 0.00 0.00 0.00 4.45
1778 1874 0.033699 GTACAGGTACCTCCGGTCCT 60.034 60.000 12.84 0.08 43.20 3.85
1926 2025 1.298014 GGTGGAGAAGACCTGCAGG 59.702 63.158 31.60 31.60 44.12 4.85
2122 2222 3.884693 TCTACACACTGTACGACTCCAAA 59.115 43.478 0.00 0.00 0.00 3.28
2135 2235 4.594675 ACTCCTATCCTGTCTACACACT 57.405 45.455 0.00 0.00 0.00 3.55
2201 2302 1.919240 ACATCGTGTGTCTACCTCCA 58.081 50.000 0.00 0.00 35.77 3.86
2311 2416 1.461091 TACGGACGCTCATCCCCATC 61.461 60.000 0.00 0.00 35.03 3.51
2319 2424 1.138883 GCATGACTACGGACGCTCA 59.861 57.895 0.00 0.00 0.00 4.26
2365 2470 3.985925 GACACCGAGATTTGTTAACGAGT 59.014 43.478 0.26 0.00 0.00 4.18
2543 2651 2.154462 CTCCTGAAATTGTGCGAACCT 58.846 47.619 0.00 0.00 0.00 3.50
2576 2684 1.763968 TCACCTGACGATCTCCGAAT 58.236 50.000 0.00 0.00 41.76 3.34
2658 2766 2.732468 CGCCGAGATCCGCATCTG 60.732 66.667 0.00 0.00 39.71 2.90
2831 2939 2.355837 TCACGTCCTTCAGTGCGC 60.356 61.111 0.00 0.00 38.19 6.09


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

AutoCloner maintained by Alex Coulton.