Multiple sequence alignment - TraesCS2B01G172700

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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 TraesCS2B01G172700 chr2B 100.000 3750 0 0 1 3750 146903851 146907600 0.000000e+00 6926.0
1 TraesCS2B01G172700 chr2B 100.000 51 0 0 2147 2197 146905786 146905836 1.110000e-15 95.3
2 TraesCS2B01G172700 chr2B 100.000 51 0 0 1936 1986 146905997 146906047 1.110000e-15 95.3
3 TraesCS2B01G172700 chr2A 89.784 3563 218 63 1 3508 93929542 93933013 0.000000e+00 4429.0
4 TraesCS2B01G172700 chr2A 96.296 54 2 0 2143 2196 93931506 93931559 5.160000e-14 89.8
5 TraesCS2B01G172700 chr2A 96.154 52 2 0 79 130 93929538 93929589 6.670000e-13 86.1
6 TraesCS2B01G172700 chr2D 88.576 3160 215 77 1 3122 95412905 95415956 0.000000e+00 3701.0
7 TraesCS2B01G172700 chr2D 85.606 396 45 11 691 1075 185006496 185006102 4.510000e-109 405.0
8 TraesCS2B01G172700 chr2D 90.196 51 4 1 2144 2194 95414827 95414876 8.690000e-07 65.8
9 TraesCS2B01G172700 chr1A 89.134 635 53 10 3123 3750 268120109 268120734 0.000000e+00 776.0
10 TraesCS2B01G172700 chrUn 88.850 574 52 10 3123 3692 144789677 144789112 0.000000e+00 695.0
11 TraesCS2B01G172700 chrUn 88.235 578 52 10 3123 3692 144752612 144752043 0.000000e+00 676.0
12 TraesCS2B01G172700 chrUn 87.905 587 55 13 3123 3701 144821991 144821413 0.000000e+00 676.0
13 TraesCS2B01G172700 chrUn 88.235 578 52 13 3123 3692 421553779 421554348 0.000000e+00 676.0
14 TraesCS2B01G172700 chrUn 88.194 576 54 12 3123 3692 179823982 179823415 0.000000e+00 675.0
15 TraesCS2B01G172700 chrUn 86.144 599 55 16 3123 3701 12083159 12082569 4.110000e-174 621.0
16 TraesCS2B01G172700 chrUn 86.271 590 53 16 3123 3692 12079191 12078610 1.910000e-172 616.0
17 TraesCS2B01G172700 chr5A 88.408 578 50 11 3123 3692 7756645 7756077 0.000000e+00 680.0
18 TraesCS2B01G172700 chr1B 88.826 528 43 9 3123 3648 303227213 303226700 5.280000e-178 634.0
19 TraesCS2B01G172700 chr7B 78.806 335 58 10 3426 3750 591672216 591671885 2.930000e-51 213.0


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 TraesCS2B01G172700 chr2B 146903851 146907600 3749 False 2372.200000 6926 100.0000 1 3750 3 chr2B.!!$F1 3749
1 TraesCS2B01G172700 chr2A 93929538 93933013 3475 False 1534.966667 4429 94.0780 1 3508 3 chr2A.!!$F1 3507
2 TraesCS2B01G172700 chr2D 95412905 95415956 3051 False 1883.400000 3701 89.3860 1 3122 2 chr2D.!!$F1 3121
3 TraesCS2B01G172700 chr1A 268120109 268120734 625 False 776.000000 776 89.1340 3123 3750 1 chr1A.!!$F1 627
4 TraesCS2B01G172700 chrUn 144789112 144789677 565 True 695.000000 695 88.8500 3123 3692 1 chrUn.!!$R2 569
5 TraesCS2B01G172700 chrUn 144752043 144752612 569 True 676.000000 676 88.2350 3123 3692 1 chrUn.!!$R1 569
6 TraesCS2B01G172700 chrUn 144821413 144821991 578 True 676.000000 676 87.9050 3123 3701 1 chrUn.!!$R3 578
7 TraesCS2B01G172700 chrUn 421553779 421554348 569 False 676.000000 676 88.2350 3123 3692 1 chrUn.!!$F1 569
8 TraesCS2B01G172700 chrUn 179823415 179823982 567 True 675.000000 675 88.1940 3123 3692 1 chrUn.!!$R4 569
9 TraesCS2B01G172700 chrUn 12078610 12083159 4549 True 618.500000 621 86.2075 3123 3701 2 chrUn.!!$R5 578
10 TraesCS2B01G172700 chr5A 7756077 7756645 568 True 680.000000 680 88.4080 3123 3692 1 chr5A.!!$R1 569
11 TraesCS2B01G172700 chr1B 303226700 303227213 513 True 634.000000 634 88.8260 3123 3648 1 chr1B.!!$R1 525

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
958 985 0.099082 GAGCGTAGAGGTCAGGAACG 59.901 60.0 0.00 0.00 46.08 3.95 F
1065 1092 0.036858 GGTGAGGCTCCAAGACTGAC 60.037 60.0 12.86 0.11 36.68 3.51 F
1067 1094 0.827925 TGAGGCTCCAAGACTGACGT 60.828 55.0 12.86 0.00 30.20 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1876 0.186873 CCTCAGGGGCCTGCAATAAT 59.813 55.0 0.84 0.0 43.31 1.28 R
2465 2528 0.250858 CACATGGACCCTGAGTTGCA 60.251 55.0 3.49 0.0 0.00 4.08 R
2862 2929 0.966179 TCTAACGGAGCAGCAGTCAA 59.034 50.0 0.00 0.0 0.00 3.18 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
41 46 7.296660 CAAACAAGCACAGAATTCAACAAAAA 58.703 30.769 8.44 0.00 0.00 1.94
61 66 9.275398 ACAAAAATTACTATCGACACAACCTAA 57.725 29.630 0.00 0.00 0.00 2.69
179 184 4.019681 TGGATTGGTTCCTTACACTGGTAG 60.020 45.833 0.00 0.00 45.68 3.18
235 240 7.625606 GCAATTAGCTTGGTACTGTTCGTATTT 60.626 37.037 0.00 0.00 41.15 1.40
237 242 4.000988 AGCTTGGTACTGTTCGTATTTGG 58.999 43.478 0.00 0.00 0.00 3.28
242 247 3.499157 GGTACTGTTCGTATTTGGTTGCA 59.501 43.478 0.00 0.00 0.00 4.08
368 376 3.827898 CCCGAGCTCCCTCACGAC 61.828 72.222 8.47 0.00 38.00 4.34
384 392 2.157668 CACGACCTTGTGGAAATCGAAG 59.842 50.000 0.00 0.00 36.20 3.79
513 521 4.242586 TCCCAGTCGTCCCACCCA 62.243 66.667 0.00 0.00 0.00 4.51
520 531 3.480133 CGTCCCACCCATCCTCCC 61.480 72.222 0.00 0.00 0.00 4.30
558 569 1.075425 CGTCGTCCTCGTAGTCGTCT 61.075 60.000 0.00 0.00 38.33 4.18
634 646 0.968405 GGCCAATTGCTTCTTGGTGA 59.032 50.000 0.00 0.00 44.17 4.02
673 685 0.819582 CGGCTCGGTTAAACCCTAGA 59.180 55.000 0.00 0.00 33.75 2.43
703 716 1.153289 CCCTGGACGAATGAGGCTG 60.153 63.158 0.00 0.00 0.00 4.85
714 727 2.440980 GAGGCTGGTGAATGGGCC 60.441 66.667 0.00 0.00 44.38 5.80
729 742 2.112297 GCCGGGCCGAATATCCAA 59.888 61.111 30.79 0.00 0.00 3.53
764 787 1.538666 GGCCCAGCCCATAAGATGT 59.461 57.895 0.00 0.00 44.06 3.06
796 820 1.202582 CGAGTCTCCGGTCTCAACAAT 59.797 52.381 18.26 0.00 0.00 2.71
825 849 2.364317 CTCGCCCCCTTCCTCTCA 60.364 66.667 0.00 0.00 0.00 3.27
890 914 1.400737 CTACCCGGTCCAGGTAAGAG 58.599 60.000 5.48 0.00 39.36 2.85
912 937 1.933051 TCTCTCATCTCCTCTTCCCCA 59.067 52.381 0.00 0.00 0.00 4.96
918 945 0.105964 TCTCCTCTTCCCCATCCTCG 60.106 60.000 0.00 0.00 0.00 4.63
945 972 4.573607 TCGAGCTTGTAAGAATAGAGCGTA 59.426 41.667 0.00 0.00 38.34 4.42
958 985 0.099082 GAGCGTAGAGGTCAGGAACG 59.901 60.000 0.00 0.00 46.08 3.95
972 999 1.112113 GGAACGGCACTGATAGAGGA 58.888 55.000 0.00 0.00 0.00 3.71
1065 1092 0.036858 GGTGAGGCTCCAAGACTGAC 60.037 60.000 12.86 0.11 36.68 3.51
1067 1094 0.827925 TGAGGCTCCAAGACTGACGT 60.828 55.000 12.86 0.00 30.20 4.34
1116 1145 1.374190 CCCTTGAGCTCACTGTGCT 59.626 57.895 18.03 5.28 44.24 4.40
1211 1240 4.864334 CCAGGGTGCGAGGATGGC 62.864 72.222 0.00 0.00 41.71 4.40
1215 1244 2.203070 GGTGCGAGGATGGCGAAT 60.203 61.111 0.00 0.00 45.68 3.34
1278 1307 2.032528 CTGGACAGGAGCGGCAAA 59.967 61.111 1.45 0.00 0.00 3.68
1312 1341 2.684843 CGGCTGCTGTCCTTTCTGC 61.685 63.158 0.00 0.00 0.00 4.26
1384 1413 1.032794 CGTCGGGAAGATGATCTCCA 58.967 55.000 0.00 0.00 38.11 3.86
1386 1415 1.069358 GTCGGGAAGATGATCTCCACC 59.931 57.143 0.00 0.23 0.00 4.61
1468 1497 2.543653 CGCTGGGAGAAAAGGTTTGTTG 60.544 50.000 0.00 0.00 0.00 3.33
1469 1498 2.430694 GCTGGGAGAAAAGGTTTGTTGT 59.569 45.455 0.00 0.00 0.00 3.32
1483 1516 7.164230 AGGTTTGTTGTTGTTGTGAAATCTA 57.836 32.000 0.00 0.00 0.00 1.98
1485 1518 8.257306 AGGTTTGTTGTTGTTGTGAAATCTAAT 58.743 29.630 0.00 0.00 0.00 1.73
1491 1524 9.509855 GTTGTTGTTGTGAAATCTAATTGTGTA 57.490 29.630 0.00 0.00 0.00 2.90
1512 1545 6.201806 GTGTACAATCTGATAGTGATTCAGGC 59.798 42.308 0.00 0.00 40.80 4.85
1513 1546 4.712476 ACAATCTGATAGTGATTCAGGCC 58.288 43.478 0.00 0.00 40.80 5.19
1534 1567 4.076394 CCGAAAAGAATTCTTGGGTGGTA 58.924 43.478 21.15 0.00 36.12 3.25
1584 1617 8.493547 CACACTATATGCAATAGTTCAGATGTG 58.506 37.037 14.86 14.23 32.93 3.21
1704 1737 2.969628 ACTCTTATTCTGGAGTGGCG 57.030 50.000 0.00 0.00 40.71 5.69
1918 1979 7.154191 TGCTCCTAATTCTTCCTATGGATTT 57.846 36.000 0.00 0.00 0.00 2.17
1933 1994 9.288576 TCCTATGGATTTAAAGCAACTGATATG 57.711 33.333 5.72 0.00 0.00 1.78
1990 2051 4.899616 GCTTTTGTGCATTTGAATTGTTCG 59.100 37.500 0.00 0.00 0.00 3.95
1994 2055 4.047822 TGTGCATTTGAATTGTTCGGTTC 58.952 39.130 0.00 0.00 0.00 3.62
2002 2063 4.258543 TGAATTGTTCGGTTCCCTCATAC 58.741 43.478 0.00 0.00 0.00 2.39
2011 2072 2.158755 GGTTCCCTCATACTGGGTGATG 60.159 54.545 0.00 0.00 44.84 3.07
2014 2075 4.485653 TCCCTCATACTGGGTGATGATA 57.514 45.455 0.00 0.00 44.84 2.15
2150 2211 7.944729 ATTGTATGTCATTCTGCTTAAGGTT 57.055 32.000 4.29 0.00 0.00 3.50
2151 2212 9.461312 AATTGTATGTCATTCTGCTTAAGGTTA 57.539 29.630 4.29 0.00 0.00 2.85
2152 2213 9.632638 ATTGTATGTCATTCTGCTTAAGGTTAT 57.367 29.630 4.29 0.00 0.00 1.89
2153 2214 8.437360 TGTATGTCATTCTGCTTAAGGTTATG 57.563 34.615 4.29 0.00 0.00 1.90
2154 2215 5.818136 TGTCATTCTGCTTAAGGTTATGC 57.182 39.130 4.29 1.60 35.20 3.14
2156 2217 5.887598 TGTCATTCTGCTTAAGGTTATGCAT 59.112 36.000 3.79 3.79 41.19 3.96
2157 2218 6.377996 TGTCATTCTGCTTAAGGTTATGCATT 59.622 34.615 3.54 0.00 41.19 3.56
2158 2219 6.694411 GTCATTCTGCTTAAGGTTATGCATTG 59.306 38.462 3.54 8.76 41.19 2.82
2159 2220 4.637483 TCTGCTTAAGGTTATGCATTGC 57.363 40.909 3.54 0.46 41.19 3.56
2160 2221 4.272489 TCTGCTTAAGGTTATGCATTGCT 58.728 39.130 3.54 0.00 41.19 3.91
2161 2222 4.706476 TCTGCTTAAGGTTATGCATTGCTT 59.294 37.500 3.54 6.23 41.19 3.91
2162 2223 4.746729 TGCTTAAGGTTATGCATTGCTTG 58.253 39.130 3.54 0.00 38.42 4.01
2163 2224 4.220382 TGCTTAAGGTTATGCATTGCTTGT 59.780 37.500 3.54 0.00 38.42 3.16
2165 2226 6.071672 TGCTTAAGGTTATGCATTGCTTGTAA 60.072 34.615 3.54 4.23 38.42 2.41
2166 2227 6.980397 GCTTAAGGTTATGCATTGCTTGTAAT 59.020 34.615 3.54 0.00 34.87 1.89
2167 2228 7.043192 GCTTAAGGTTATGCATTGCTTGTAATG 60.043 37.037 3.54 7.00 40.25 1.90
2179 2240 6.890663 TTGCTTGTAATGCTTATTTCATGC 57.109 33.333 0.00 0.00 37.94 4.06
2180 2241 6.211587 TGCTTGTAATGCTTATTTCATGCT 57.788 33.333 14.01 0.00 37.94 3.79
2181 2242 6.632909 TGCTTGTAATGCTTATTTCATGCTT 58.367 32.000 14.01 0.00 37.94 3.91
2182 2243 7.098477 TGCTTGTAATGCTTATTTCATGCTTT 58.902 30.769 14.01 0.00 37.94 3.51
2183 2244 7.603404 TGCTTGTAATGCTTATTTCATGCTTTT 59.397 29.630 14.01 0.00 37.94 2.27
2184 2245 7.901377 GCTTGTAATGCTTATTTCATGCTTTTG 59.099 33.333 0.00 0.00 32.92 2.44
2185 2246 8.830201 TTGTAATGCTTATTTCATGCTTTTGT 57.170 26.923 0.00 0.00 0.00 2.83
2186 2247 8.242085 TGTAATGCTTATTTCATGCTTTTGTG 57.758 30.769 0.00 0.00 0.00 3.33
2187 2248 5.789710 ATGCTTATTTCATGCTTTTGTGC 57.210 34.783 0.00 0.00 0.00 4.57
2425 2487 6.220201 GGTAACTTATGCCACACAAAAATGT 58.780 36.000 0.00 0.00 33.24 2.71
2426 2488 6.704050 GGTAACTTATGCCACACAAAAATGTT 59.296 34.615 0.00 0.00 33.24 2.71
2458 2521 1.402720 CCCTGTATTTGCTTTGCCACG 60.403 52.381 0.00 0.00 0.00 4.94
2463 2526 0.936600 ATTTGCTTTGCCACGTTTGC 59.063 45.000 0.00 0.00 0.00 3.68
2465 2528 0.108424 TTGCTTTGCCACGTTTGCTT 60.108 45.000 8.18 0.00 0.00 3.91
2475 2538 0.381801 ACGTTTGCTTGCAACTCAGG 59.618 50.000 7.60 2.59 0.00 3.86
2545 2608 7.595502 AGCAGTATACATGTCTAGAATTTACGC 59.404 37.037 0.00 2.53 0.00 4.42
2555 2619 7.349711 TGTCTAGAATTTACGCAAGAACAAAC 58.650 34.615 0.00 0.00 43.62 2.93
2567 2631 1.850345 AGAACAAACTGAGGAACCCCA 59.150 47.619 0.00 0.00 33.88 4.96
2570 2634 0.478507 CAAACTGAGGAACCCCACCT 59.521 55.000 0.00 0.00 40.80 4.00
2588 2652 4.524328 CCACCTTAGATTCTTTTGCAACCT 59.476 41.667 0.00 0.00 0.00 3.50
2630 2695 5.531634 TGGCTTACTGCATTTCTTTTTCTG 58.468 37.500 0.00 0.00 45.15 3.02
2642 2707 7.428020 CATTTCTTTTTCTGTCATGAAGGTCA 58.572 34.615 0.00 0.00 0.00 4.02
2781 2846 4.685924 GATGAAATGCCAAACCACATAGG 58.314 43.478 0.00 0.00 45.67 2.57
2807 2872 5.594725 ACATCGGCAAGATCTCTCTTTAGTA 59.405 40.000 0.00 0.00 39.78 1.82
2860 2927 1.599071 AGTGTGTGATTGACTGTTGCG 59.401 47.619 0.00 0.00 0.00 4.85
2861 2928 1.597195 GTGTGTGATTGACTGTTGCGA 59.403 47.619 0.00 0.00 0.00 5.10
2862 2929 2.224079 GTGTGTGATTGACTGTTGCGAT 59.776 45.455 0.00 0.00 0.00 4.58
2863 2930 2.877786 TGTGTGATTGACTGTTGCGATT 59.122 40.909 0.00 0.00 0.00 3.34
2864 2931 3.228749 GTGTGATTGACTGTTGCGATTG 58.771 45.455 0.00 0.00 0.00 2.67
2865 2932 3.058983 GTGTGATTGACTGTTGCGATTGA 60.059 43.478 0.00 0.00 0.00 2.57
2866 2933 3.058983 TGTGATTGACTGTTGCGATTGAC 60.059 43.478 0.00 0.00 0.00 3.18
2867 2934 3.187227 GTGATTGACTGTTGCGATTGACT 59.813 43.478 0.00 0.00 0.00 3.41
2868 2935 3.187022 TGATTGACTGTTGCGATTGACTG 59.813 43.478 0.00 0.00 0.00 3.51
2869 2936 0.867746 TGACTGTTGCGATTGACTGC 59.132 50.000 0.00 0.00 0.00 4.40
2870 2937 1.151668 GACTGTTGCGATTGACTGCT 58.848 50.000 0.00 0.00 0.00 4.24
2871 2938 0.870393 ACTGTTGCGATTGACTGCTG 59.130 50.000 0.00 0.00 0.00 4.41
2872 2939 0.453950 CTGTTGCGATTGACTGCTGC 60.454 55.000 0.00 0.00 0.00 5.25
2905 2972 6.525121 TCTCTTTTAAGTGTGTGATTGACG 57.475 37.500 0.00 0.00 0.00 4.35
2906 2973 6.277605 TCTCTTTTAAGTGTGTGATTGACGA 58.722 36.000 0.00 0.00 0.00 4.20
2907 2974 6.200286 TCTCTTTTAAGTGTGTGATTGACGAC 59.800 38.462 0.00 0.00 0.00 4.34
2926 2993 5.437946 ACGACTGTTACTCTGGATGAGATA 58.562 41.667 0.00 0.00 45.39 1.98
2933 3000 3.585360 ACTCTGGATGAGATACAGGCAT 58.415 45.455 0.00 0.00 45.39 4.40
3085 3156 6.407752 CCCACGGAACTTTATATAGTGGTCTT 60.408 42.308 10.29 0.00 44.27 3.01
3174 3246 4.746535 TGGAAGTGTGTCAGTTTAGTCA 57.253 40.909 0.00 0.00 0.00 3.41
3223 3295 5.514310 GGTCCTAAAACTATTGGAGGTGTGT 60.514 44.000 0.00 0.00 0.00 3.72
3226 3298 6.001460 CCTAAAACTATTGGAGGTGTGTCAA 58.999 40.000 0.00 0.00 0.00 3.18
3395 3468 1.663695 CACCAAGTTGACTTCCACGT 58.336 50.000 3.87 0.00 33.11 4.49
3396 3469 1.597663 CACCAAGTTGACTTCCACGTC 59.402 52.381 3.87 0.00 33.11 4.34
3397 3470 0.859232 CCAAGTTGACTTCCACGTCG 59.141 55.000 3.87 0.00 36.71 5.12
3398 3471 1.567504 CAAGTTGACTTCCACGTCGT 58.432 50.000 0.00 0.00 36.71 4.34
3399 3472 1.521423 CAAGTTGACTTCCACGTCGTC 59.479 52.381 0.00 0.00 36.71 4.20
3400 3473 0.031721 AGTTGACTTCCACGTCGTCC 59.968 55.000 0.00 0.00 36.71 4.79
3401 3474 1.008194 TTGACTTCCACGTCGTCCG 60.008 57.895 0.00 0.00 44.03 4.79
3421 3494 1.136984 CGTCCCGCAGTAGTGACTC 59.863 63.158 0.42 0.00 31.73 3.36
3441 3514 0.324552 TTTCCCATCTGTGGCCATGG 60.325 55.000 9.72 13.11 44.62 3.66
3485 3558 2.265367 TGACCAACTCTATGGCAAGGA 58.735 47.619 0.00 0.00 44.75 3.36
3502 3575 0.693049 GGATATCGGGGCAAGGACAT 59.307 55.000 0.00 0.00 0.00 3.06
3525 3615 1.133513 TCATGAGAGAGAGAGAGGGGC 60.134 57.143 0.00 0.00 0.00 5.80
3606 3697 1.077501 ATGTTGTCCTCCATGCCGG 60.078 57.895 0.00 0.00 0.00 6.13
3706 3799 4.400410 GCAGGTTGCAACACACAC 57.600 55.556 29.55 12.81 44.26 3.82
3708 3801 0.526096 GCAGGTTGCAACACACACTG 60.526 55.000 29.55 24.95 44.26 3.66
3709 3802 0.526096 CAGGTTGCAACACACACTGC 60.526 55.000 29.55 10.66 39.09 4.40
3713 3806 1.301677 TTGCAACACACACTGCGACA 61.302 50.000 0.00 0.00 41.63 4.35
3731 3824 3.206150 GACATTGAAGCGTATGGACCAT 58.794 45.455 12.67 12.67 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 11 1.042229 TGCTTGTTTGCTGCATTCCT 58.958 45.000 1.84 0.00 0.00 3.36
53 58 9.574516 GGACCTTATGATTGATATTTAGGTTGT 57.425 33.333 0.00 0.00 35.04 3.32
61 66 8.393259 TGGCTTATGGACCTTATGATTGATATT 58.607 33.333 0.00 0.00 0.00 1.28
169 174 2.947652 GTCGTATGAGGCTACCAGTGTA 59.052 50.000 0.00 0.00 0.00 2.90
179 184 2.423577 ACTTTTGTGGTCGTATGAGGC 58.576 47.619 0.00 0.00 0.00 4.70
220 225 3.499157 TGCAACCAAATACGAACAGTACC 59.501 43.478 0.00 0.00 38.29 3.34
222 227 5.512473 GTTTGCAACCAAATACGAACAGTA 58.488 37.500 0.00 0.00 42.44 2.74
237 242 1.266718 TCAGCTCGATTGGTTTGCAAC 59.733 47.619 0.00 0.00 0.00 4.17
242 247 2.079925 GCTTCTCAGCTCGATTGGTTT 58.920 47.619 0.00 0.00 43.51 3.27
368 376 0.447801 CGGCTTCGATTTCCACAAGG 59.552 55.000 0.00 0.00 35.61 3.61
513 521 2.416923 GGAGGAGGAGGGGGAGGAT 61.417 68.421 0.00 0.00 0.00 3.24
520 531 0.178935 GAGGATGAGGAGGAGGAGGG 60.179 65.000 0.00 0.00 0.00 4.30
673 685 0.036294 GTCCAGGGCTTAAGCTTCGT 60.036 55.000 25.88 9.95 41.70 3.85
714 727 1.806542 CTCATTTGGATATTCGGCCCG 59.193 52.381 0.00 0.00 0.00 6.13
721 734 4.078980 ACCTTCCAGCCTCATTTGGATATT 60.079 41.667 0.00 0.00 42.73 1.28
722 735 3.464833 ACCTTCCAGCCTCATTTGGATAT 59.535 43.478 0.00 0.00 42.73 1.63
723 736 2.852449 ACCTTCCAGCCTCATTTGGATA 59.148 45.455 0.00 0.00 42.73 2.59
724 737 1.642762 ACCTTCCAGCCTCATTTGGAT 59.357 47.619 0.00 0.00 42.73 3.41
725 738 1.075601 ACCTTCCAGCCTCATTTGGA 58.924 50.000 0.00 0.00 41.59 3.53
726 739 1.180029 CACCTTCCAGCCTCATTTGG 58.820 55.000 0.00 0.00 35.74 3.28
727 740 1.180029 CCACCTTCCAGCCTCATTTG 58.820 55.000 0.00 0.00 0.00 2.32
729 742 1.693640 CCCACCTTCCAGCCTCATT 59.306 57.895 0.00 0.00 0.00 2.57
751 774 5.071115 GGTCTTCTCTAACATCTTATGGGCT 59.929 44.000 0.00 0.00 33.60 5.19
791 814 0.391263 GAGACGAAGGGCGGATTGTT 60.391 55.000 0.00 0.00 46.49 2.83
858 882 4.549516 GGTAGCGTCGGACGGCTC 62.550 72.222 29.30 14.57 42.82 4.70
868 892 2.786512 TTACCTGGACCGGGTAGCGT 62.787 60.000 27.63 8.34 44.89 5.07
879 903 3.204158 AGATGAGAGAGCTCTTACCTGGA 59.796 47.826 19.36 0.00 40.61 3.86
890 914 1.963515 GGGAAGAGGAGATGAGAGAGC 59.036 57.143 0.00 0.00 0.00 4.09
918 945 1.641577 ATTCTTACAAGCTCGACGGC 58.358 50.000 0.00 0.00 0.00 5.68
925 952 5.009210 CCTCTACGCTCTATTCTTACAAGCT 59.991 44.000 0.00 0.00 0.00 3.74
945 972 1.534235 AGTGCCGTTCCTGACCTCT 60.534 57.895 0.00 0.00 0.00 3.69
958 985 1.112113 TTCCGTCCTCTATCAGTGCC 58.888 55.000 0.00 0.00 0.00 5.01
1065 1092 2.156917 GGACTTTGGTTAAGGGGAACG 58.843 52.381 0.00 0.00 38.23 3.95
1067 1094 1.546099 GCGGACTTTGGTTAAGGGGAA 60.546 52.381 0.00 0.00 38.23 3.97
1211 1240 3.876198 CCTTTCCGCCGCCATTCG 61.876 66.667 0.00 0.00 38.08 3.34
1416 1445 0.911769 AGAGCAAATGGATGGTCCGA 59.088 50.000 3.14 0.00 46.41 4.55
1468 1497 9.509855 TTGTACACAATTAGATTTCACAACAAC 57.490 29.630 0.00 0.00 0.00 3.32
1483 1516 9.671279 TGAATCACTATCAGATTGTACACAATT 57.329 29.630 8.88 0.00 45.72 2.32
1485 1518 7.765819 CCTGAATCACTATCAGATTGTACACAA 59.234 37.037 0.00 0.00 45.74 3.33
1491 1524 4.712476 GGCCTGAATCACTATCAGATTGT 58.288 43.478 0.00 0.00 45.74 2.71
1512 1545 2.890945 ACCACCCAAGAATTCTTTTCGG 59.109 45.455 18.16 18.15 33.11 4.30
1513 1546 5.240844 AGTTACCACCCAAGAATTCTTTTCG 59.759 40.000 18.16 10.52 33.11 3.46
1555 1588 6.479990 TCTGAACTATTGCATATAGTGTGTGC 59.520 38.462 16.95 1.50 44.39 4.57
1556 1589 8.493547 CATCTGAACTATTGCATATAGTGTGTG 58.506 37.037 16.95 10.83 35.25 3.82
1557 1590 8.206867 ACATCTGAACTATTGCATATAGTGTGT 58.793 33.333 16.95 14.12 35.25 3.72
1584 1617 5.468072 CAGCTCCATATTCAGAACCATACAC 59.532 44.000 0.00 0.00 0.00 2.90
1704 1737 4.275936 TCAAGTCCTTTAGCAGCTGAAAAC 59.724 41.667 20.43 6.28 0.00 2.43
1781 1841 5.634896 CAATACTTGTCAGCATTTCAGACC 58.365 41.667 0.00 0.00 30.97 3.85
1784 1844 4.157289 AGGCAATACTTGTCAGCATTTCAG 59.843 41.667 0.00 0.00 37.85 3.02
1815 1876 0.186873 CCTCAGGGGCCTGCAATAAT 59.813 55.000 0.84 0.00 43.31 1.28
1818 1879 2.551413 AACCTCAGGGGCCTGCAAT 61.551 57.895 0.84 0.00 43.31 3.56
1918 1979 7.990314 TGCATAACCTACATATCAGTTGCTTTA 59.010 33.333 0.00 0.00 0.00 1.85
2002 2063 3.713902 GGTGGCTATCATCACCCAG 57.286 57.895 0.00 0.00 45.60 4.45
2046 2107 7.765819 CACCATCACTGAGTTTTATCTGTATGA 59.234 37.037 0.00 0.00 31.06 2.15
2154 2215 7.223971 AGCATGAAATAAGCATTACAAGCAATG 59.776 33.333 0.00 0.00 38.65 2.82
2156 2217 6.632909 AGCATGAAATAAGCATTACAAGCAA 58.367 32.000 0.00 0.00 30.46 3.91
2157 2218 6.211587 AGCATGAAATAAGCATTACAAGCA 57.788 33.333 0.00 0.00 30.46 3.91
2158 2219 7.529880 AAAGCATGAAATAAGCATTACAAGC 57.470 32.000 0.00 0.00 30.46 4.01
2159 2220 8.928733 ACAAAAGCATGAAATAAGCATTACAAG 58.071 29.630 0.00 0.00 30.46 3.16
2160 2221 8.710551 CACAAAAGCATGAAATAAGCATTACAA 58.289 29.630 0.00 0.00 30.46 2.41
2161 2222 7.148606 GCACAAAAGCATGAAATAAGCATTACA 60.149 33.333 0.00 0.00 30.46 2.41
2162 2223 7.148606 TGCACAAAAGCATGAAATAAGCATTAC 60.149 33.333 0.00 0.00 40.11 1.89
2163 2224 6.872547 TGCACAAAAGCATGAAATAAGCATTA 59.127 30.769 0.00 0.00 40.11 1.90
2165 2226 5.239351 TGCACAAAAGCATGAAATAAGCAT 58.761 33.333 0.00 0.00 40.11 3.79
2166 2227 4.629092 TGCACAAAAGCATGAAATAAGCA 58.371 34.783 0.00 0.00 40.11 3.91
2178 2239 5.397240 GCAAAGAATTCAAATGCACAAAAGC 59.603 36.000 19.17 0.00 37.00 3.51
2179 2240 6.487960 TGCAAAGAATTCAAATGCACAAAAG 58.512 32.000 21.51 0.00 41.67 2.27
2180 2241 6.432607 TGCAAAGAATTCAAATGCACAAAA 57.567 29.167 21.51 6.08 41.67 2.44
2185 2246 3.808726 GGTGTGCAAAGAATTCAAATGCA 59.191 39.130 21.51 21.51 44.07 3.96
2186 2247 3.187022 GGGTGTGCAAAGAATTCAAATGC 59.813 43.478 17.95 17.95 37.52 3.56
2187 2248 4.378774 TGGGTGTGCAAAGAATTCAAATG 58.621 39.130 8.44 4.63 0.00 2.32
2188 2249 4.344679 TCTGGGTGTGCAAAGAATTCAAAT 59.655 37.500 8.44 0.00 0.00 2.32
2189 2250 3.703556 TCTGGGTGTGCAAAGAATTCAAA 59.296 39.130 8.44 0.00 0.00 2.69
2190 2251 3.295093 TCTGGGTGTGCAAAGAATTCAA 58.705 40.909 8.44 0.00 0.00 2.69
2191 2252 2.942804 TCTGGGTGTGCAAAGAATTCA 58.057 42.857 8.44 0.00 0.00 2.57
2192 2253 4.219288 AGATTCTGGGTGTGCAAAGAATTC 59.781 41.667 0.00 0.00 39.01 2.17
2204 2265 4.520492 ACTTTTTGCTACAGATTCTGGGTG 59.480 41.667 17.66 8.21 35.51 4.61
2284 2346 2.488153 GGCCGCTTTCTGAAACAGTAAT 59.512 45.455 0.00 0.00 32.61 1.89
2287 2349 1.507141 CGGCCGCTTTCTGAAACAGT 61.507 55.000 14.67 0.00 32.61 3.55
2425 2487 2.561209 TACAGGGCCCTATGTCAGAA 57.439 50.000 28.13 1.56 0.00 3.02
2426 2488 2.795291 ATACAGGGCCCTATGTCAGA 57.205 50.000 28.13 5.70 0.00 3.27
2458 2521 0.746659 ACCCTGAGTTGCAAGCAAAC 59.253 50.000 9.32 7.54 37.70 2.93
2463 2526 1.171308 CATGGACCCTGAGTTGCAAG 58.829 55.000 0.00 0.00 0.00 4.01
2465 2528 0.250858 CACATGGACCCTGAGTTGCA 60.251 55.000 3.49 0.00 0.00 4.08
2475 2538 6.295349 CCTTGACTATATACCTCACATGGACC 60.295 46.154 0.00 0.00 0.00 4.46
2543 2606 2.287009 GGTTCCTCAGTTTGTTCTTGCG 60.287 50.000 0.00 0.00 0.00 4.85
2545 2608 2.623416 GGGGTTCCTCAGTTTGTTCTTG 59.377 50.000 0.00 0.00 0.00 3.02
2555 2619 1.952621 TCTAAGGTGGGGTTCCTCAG 58.047 55.000 0.00 0.00 33.76 3.35
2567 2631 6.731292 AAAGGTTGCAAAAGAATCTAAGGT 57.269 33.333 0.00 0.00 0.00 3.50
2630 2695 3.185246 ACCATCGATGACCTTCATGAC 57.815 47.619 26.86 0.00 37.20 3.06
2781 2846 1.202510 AGAGAGATCTTGCCGATGTGC 60.203 52.381 0.00 0.00 30.84 4.57
2807 2872 3.748083 ACAGAGCAACAGTCAATCACAT 58.252 40.909 0.00 0.00 0.00 3.21
2860 2927 1.929836 CTAACGGAGCAGCAGTCAATC 59.070 52.381 0.00 0.00 0.00 2.67
2861 2928 1.550524 TCTAACGGAGCAGCAGTCAAT 59.449 47.619 0.00 0.00 0.00 2.57
2862 2929 0.966179 TCTAACGGAGCAGCAGTCAA 59.034 50.000 0.00 0.00 0.00 3.18
2863 2930 1.135139 GATCTAACGGAGCAGCAGTCA 59.865 52.381 0.00 0.00 0.00 3.41
2864 2931 1.407258 AGATCTAACGGAGCAGCAGTC 59.593 52.381 0.00 0.00 31.91 3.51
2865 2932 1.407258 GAGATCTAACGGAGCAGCAGT 59.593 52.381 0.00 0.00 31.91 4.40
2866 2933 1.680735 AGAGATCTAACGGAGCAGCAG 59.319 52.381 0.00 0.00 31.91 4.24
2867 2934 1.769026 AGAGATCTAACGGAGCAGCA 58.231 50.000 0.00 0.00 31.91 4.41
2868 2935 2.880963 AAGAGATCTAACGGAGCAGC 57.119 50.000 0.00 0.00 31.91 5.25
2869 2936 6.254589 CACTTAAAAGAGATCTAACGGAGCAG 59.745 42.308 0.00 0.00 31.91 4.24
2870 2937 6.100004 CACTTAAAAGAGATCTAACGGAGCA 58.900 40.000 0.00 0.00 31.91 4.26
2871 2938 6.035112 CACACTTAAAAGAGATCTAACGGAGC 59.965 42.308 0.00 0.00 0.00 4.70
2872 2939 7.062371 CACACACTTAAAAGAGATCTAACGGAG 59.938 40.741 0.00 0.00 0.00 4.63
2905 2972 6.238897 CCTGTATCTCATCCAGAGTAACAGTC 60.239 46.154 18.66 0.00 45.80 3.51
2906 2973 5.596361 CCTGTATCTCATCCAGAGTAACAGT 59.404 44.000 18.66 0.00 45.80 3.55
2907 2974 5.508825 GCCTGTATCTCATCCAGAGTAACAG 60.509 48.000 15.84 15.84 46.24 3.16
2926 2993 4.218312 GGGGAAAGAAATGATATGCCTGT 58.782 43.478 0.00 0.00 0.00 4.00
2933 3000 8.694540 CACACATAAATGGGGAAAGAAATGATA 58.305 33.333 0.00 0.00 34.87 2.15
3060 3131 5.070047 AGACCACTATATAAAGTTCCGTGGG 59.930 44.000 15.60 0.07 43.45 4.61
3064 3135 7.222224 GTCACAAGACCACTATATAAAGTTCCG 59.778 40.741 0.00 0.00 38.89 4.30
3085 3156 3.619733 GCCAGATTCAGTACATGGTCACA 60.620 47.826 0.00 0.00 33.42 3.58
3174 3246 8.665685 CCTAAAACTGCAGTTTCGAAGTTATAT 58.334 33.333 37.59 23.11 46.47 0.86
3284 3357 3.374764 TGCAAGCTTAGGACCTGAGATA 58.625 45.455 17.24 0.00 0.00 1.98
3334 3407 4.501071 GCAACAATTCAAGCATCTCCAAT 58.499 39.130 0.00 0.00 0.00 3.16
3381 3454 0.031721 GGACGACGTGGAAGTCAACT 59.968 55.000 4.58 0.00 40.98 3.16
3459 3532 2.954318 GCCATAGAGTTGGTCATGCATT 59.046 45.455 0.00 0.00 39.11 3.56
3485 3558 1.494721 ACAATGTCCTTGCCCCGATAT 59.505 47.619 0.00 0.00 38.50 1.63
3502 3575 3.626983 CCCCTCTCTCTCTCTCATGACAA 60.627 52.174 0.00 0.00 0.00 3.18
3628 3720 0.953960 CTAAGAGGTTTTGGCGCGGT 60.954 55.000 8.83 0.00 0.00 5.68
3679 3772 2.757099 CAACCTGCATGCCCTCCC 60.757 66.667 16.68 0.00 0.00 4.30
3705 3798 1.660607 CATACGCTTCAATGTCGCAGT 59.339 47.619 0.00 0.00 0.00 4.40
3706 3799 1.004610 CCATACGCTTCAATGTCGCAG 60.005 52.381 0.00 0.00 0.00 5.18
3708 3801 1.004927 GTCCATACGCTTCAATGTCGC 60.005 52.381 0.00 0.00 0.00 5.19
3709 3802 1.593006 GGTCCATACGCTTCAATGTCG 59.407 52.381 0.00 0.00 0.00 4.35
3713 3806 5.659440 AAAAATGGTCCATACGCTTCAAT 57.341 34.783 4.33 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.