Multiple sequence alignment - TraesCS4A01G183100

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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 TraesCS4A01G183100 chr4A 100.000 2336 0 0 1 2336 460447898 460450233 0.000000e+00 4314.0
1 TraesCS4A01G183100 chr4A 93.827 162 8 2 2176 2336 11366206 11366046 2.320000e-60 243.0
2 TraesCS4A01G183100 chr4A 93.865 163 6 2 2174 2335 83317243 83317084 2.320000e-60 243.0
3 TraesCS4A01G183100 chr4B 94.889 1487 48 19 698 2177 177862193 177860728 0.000000e+00 2300.0
4 TraesCS4A01G183100 chr4B 86.491 570 60 9 1 562 178063961 178063401 5.520000e-171 610.0
5 TraesCS4A01G183100 chr4D 97.323 1345 34 2 834 2177 116153897 116152554 0.000000e+00 2283.0
6 TraesCS4A01G183100 chr4D 89.394 396 28 9 1 389 116238175 116237787 9.700000e-134 486.0
7 TraesCS4A01G183100 chr4D 88.417 259 24 3 392 650 116155821 116155569 8.110000e-80 307.0
8 TraesCS4A01G183100 chr4D 94.444 90 3 2 720 807 116153985 116153896 1.130000e-28 137.0
9 TraesCS4A01G183100 chr5D 86.364 374 35 9 975 1338 249981049 249981416 6.050000e-106 394.0
10 TraesCS4A01G183100 chr5D 90.714 140 11 2 79 216 8631297 8631436 3.960000e-43 185.0
11 TraesCS4A01G183100 chr5D 91.463 82 7 0 1 82 553888469 553888388 1.900000e-21 113.0
12 TraesCS4A01G183100 chr5D 95.556 45 2 0 1 45 8631247 8631291 3.220000e-09 73.1
13 TraesCS4A01G183100 chr5A 86.290 372 38 6 974 1338 332719478 332719843 2.180000e-105 392.0
14 TraesCS4A01G183100 chr5A 93.750 160 8 2 2178 2336 570367102 570366944 3.000000e-59 239.0
15 TraesCS4A01G183100 chr5B 86.096 374 36 9 975 1338 282847332 282847699 2.810000e-104 388.0
16 TraesCS4A01G183100 chr2A 93.373 166 9 2 2173 2336 196517960 196518125 6.450000e-61 244.0
17 TraesCS4A01G183100 chr2A 91.329 173 13 2 2165 2336 88796232 88796061 3.880000e-58 235.0
18 TraesCS4A01G183100 chr6A 93.750 160 8 2 2178 2336 180309339 180309181 3.000000e-59 239.0
19 TraesCS4A01G183100 chr3A 93.750 160 9 1 2178 2336 24050368 24050527 3.000000e-59 239.0
20 TraesCS4A01G183100 chr3A 92.771 166 10 2 2173 2336 434834908 434835073 3.000000e-59 239.0
21 TraesCS4A01G183100 chr7A 93.711 159 8 2 2178 2336 572183354 572183198 1.080000e-58 237.0
22 TraesCS4A01G183100 chr2D 82.677 127 16 3 427 548 12911576 12911701 8.830000e-20 108.0


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 TraesCS4A01G183100 chr4A 460447898 460450233 2335 False 4314 4314 100.000000 1 2336 1 chr4A.!!$F1 2335
1 TraesCS4A01G183100 chr4B 177860728 177862193 1465 True 2300 2300 94.889000 698 2177 1 chr4B.!!$R1 1479
2 TraesCS4A01G183100 chr4B 178063401 178063961 560 True 610 610 86.491000 1 562 1 chr4B.!!$R2 561
3 TraesCS4A01G183100 chr4D 116152554 116155821 3267 True 909 2283 93.394667 392 2177 3 chr4D.!!$R2 1785

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
816 2384 0.179234 TCCAAACAGCACGAGGAACA 59.821 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 3753 1.195115 TCTGGATGTGCCCTAGACAC 58.805 55.0 8.47 8.47 38.55 3.67 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
36 37 9.361315 GTTTGGTAAAAAGTGACTAACAATGTT 57.639 29.630 3.43 3.43 0.00 2.71
55 56 3.057174 TGTTTTGTTCTCGCCAAACTTGT 60.057 39.130 0.00 0.00 31.88 3.16
64 65 4.213270 TCTCGCCAAACTTGTTTGACTATG 59.787 41.667 23.00 10.24 33.95 2.23
77 78 6.173339 TGTTTGACTATGAATTCCCTCTGAC 58.827 40.000 2.27 0.00 0.00 3.51
80 81 3.970640 GACTATGAATTCCCTCTGACCCT 59.029 47.826 2.27 0.00 0.00 4.34
91 92 2.026449 CCTCTGACCCTGAAGAAGCAAT 60.026 50.000 0.00 0.00 0.00 3.56
92 93 3.008330 CTCTGACCCTGAAGAAGCAATG 58.992 50.000 0.00 0.00 0.00 2.82
112 113 6.860023 GCAATGCTTTAATCTCATGTACCATC 59.140 38.462 0.00 0.00 0.00 3.51
128 129 6.168389 TGTACCATCATCATGTATGCAGATC 58.832 40.000 0.00 0.00 35.38 2.75
140 141 2.244486 TGCAGATCTGTTCTCTCCCT 57.756 50.000 23.38 0.00 29.93 4.20
152 153 1.152419 TCTCCCTGTTCGGTGGTCA 60.152 57.895 0.00 0.00 0.00 4.02
182 183 6.192773 ACCAATTCTGAACAATCTGGATGAT 58.807 36.000 0.00 0.00 36.89 2.45
207 208 6.422333 TCACAATAGGCAAAGATGACCATTA 58.578 36.000 0.00 0.00 33.81 1.90
216 217 6.593382 GGCAAAGATGACCATTAGATAGCTAG 59.407 42.308 0.00 0.00 0.00 3.42
222 223 9.099071 AGATGACCATTAGATAGCTAGTGAAAT 57.901 33.333 11.69 2.98 36.69 2.17
223 224 9.149225 GATGACCATTAGATAGCTAGTGAAATG 57.851 37.037 11.69 3.16 36.69 2.32
228 229 7.446625 CCATTAGATAGCTAGTGAAATGCCTTT 59.553 37.037 11.69 0.00 36.69 3.11
261 265 5.357032 CACTCCATCCCACATAGGTTTAAAC 59.643 44.000 9.98 9.98 34.66 2.01
263 267 6.086011 TCCATCCCACATAGGTTTAAACAT 57.914 37.500 19.57 15.30 34.66 2.71
287 291 8.714179 CATATGATGTTTTGCAAGATTGTTTGT 58.286 29.630 0.00 0.00 0.00 2.83
306 310 2.099921 TGTGGTGGGATTTTGTCGTTTG 59.900 45.455 0.00 0.00 0.00 2.93
312 316 4.741185 GTGGGATTTTGTCGTTTGTAAACC 59.259 41.667 2.19 0.00 35.51 3.27
316 320 2.994716 TTGTCGTTTGTAAACCGACG 57.005 45.000 18.22 5.86 41.16 5.12
326 334 6.031625 CGTTTGTAAACCGACGATTAAAATGG 59.968 38.462 0.00 0.00 37.69 3.16
330 338 5.952526 AAACCGACGATTAAAATGGTTCT 57.047 34.783 0.00 0.00 38.68 3.01
337 345 8.770828 CCGACGATTAAAATGGTTCTAATACAT 58.229 33.333 0.00 0.00 0.00 2.29
385 394 6.897259 TGAATACAATAGTACGGAAAGTGC 57.103 37.500 0.00 0.00 31.96 4.40
398 407 3.312421 CGGAAAGTGCTTCAGAGAAACAA 59.688 43.478 0.00 0.00 35.55 2.83
437 446 8.012957 AGAGTACAAAAATCCTATCTGACGAT 57.987 34.615 0.00 0.00 0.00 3.73
458 467 1.276622 GTTTGCTAGGAGAGGGGTGA 58.723 55.000 0.00 0.00 0.00 4.02
560 569 5.034554 ACAAAAACTGTCATGTCGCTATG 57.965 39.130 0.00 0.00 29.87 2.23
567 576 5.423015 ACTGTCATGTCGCTATGAAGAAAT 58.577 37.500 3.47 0.00 38.69 2.17
593 602 1.173043 CCCTCGCACCTAAAAATGCA 58.827 50.000 0.00 0.00 42.17 3.96
596 605 2.228822 CCTCGCACCTAAAAATGCAAGT 59.771 45.455 0.00 0.00 42.17 3.16
619 628 1.909700 ATCATTCACAAACGCCACCT 58.090 45.000 0.00 0.00 0.00 4.00
620 629 1.686355 TCATTCACAAACGCCACCTT 58.314 45.000 0.00 0.00 0.00 3.50
621 630 1.606668 TCATTCACAAACGCCACCTTC 59.393 47.619 0.00 0.00 0.00 3.46
623 632 1.757682 TTCACAAACGCCACCTTCTT 58.242 45.000 0.00 0.00 0.00 2.52
625 634 1.134220 TCACAAACGCCACCTTCTTCT 60.134 47.619 0.00 0.00 0.00 2.85
626 635 1.676006 CACAAACGCCACCTTCTTCTT 59.324 47.619 0.00 0.00 0.00 2.52
627 636 2.099098 CACAAACGCCACCTTCTTCTTT 59.901 45.455 0.00 0.00 0.00 2.52
630 639 4.399934 ACAAACGCCACCTTCTTCTTTTAA 59.600 37.500 0.00 0.00 0.00 1.52
636 645 4.738252 GCCACCTTCTTCTTTTAACAAACG 59.262 41.667 0.00 0.00 0.00 3.60
654 2191 1.377612 GTTCACCGGCTAAGGGGTT 59.622 57.895 0.00 0.00 35.77 4.11
655 2192 0.958876 GTTCACCGGCTAAGGGGTTG 60.959 60.000 0.00 0.00 35.77 3.77
668 2205 2.876581 AGGGGTTGAAAAGTAAGCCAG 58.123 47.619 8.06 0.00 45.18 4.85
671 2208 2.963101 GGGTTGAAAAGTAAGCCAGGTT 59.037 45.455 0.00 0.00 43.40 3.50
672 2209 4.146564 GGGTTGAAAAGTAAGCCAGGTTA 58.853 43.478 0.00 0.00 43.40 2.85
690 2230 6.438763 CAGGTTAATTGTCCAGTGAAGAAAC 58.561 40.000 0.00 0.00 0.00 2.78
810 2378 3.896648 GAAAGAATCCAAACAGCACGA 57.103 42.857 0.00 0.00 0.00 4.35
811 2379 3.814945 GAAAGAATCCAAACAGCACGAG 58.185 45.455 0.00 0.00 0.00 4.18
812 2380 1.813513 AGAATCCAAACAGCACGAGG 58.186 50.000 0.00 0.00 0.00 4.63
813 2381 1.347707 AGAATCCAAACAGCACGAGGA 59.652 47.619 0.00 0.00 0.00 3.71
814 2382 2.151202 GAATCCAAACAGCACGAGGAA 58.849 47.619 0.00 0.00 31.17 3.36
815 2383 1.523758 ATCCAAACAGCACGAGGAAC 58.476 50.000 0.00 0.00 31.17 3.62
816 2384 0.179234 TCCAAACAGCACGAGGAACA 59.821 50.000 0.00 0.00 0.00 3.18
817 2385 1.021202 CCAAACAGCACGAGGAACAA 58.979 50.000 0.00 0.00 0.00 2.83
818 2386 1.403679 CCAAACAGCACGAGGAACAAA 59.596 47.619 0.00 0.00 0.00 2.83
819 2387 2.450160 CAAACAGCACGAGGAACAAAC 58.550 47.619 0.00 0.00 0.00 2.93
820 2388 2.038387 AACAGCACGAGGAACAAACT 57.962 45.000 0.00 0.00 0.00 2.66
821 2389 1.299541 ACAGCACGAGGAACAAACTG 58.700 50.000 0.00 0.00 0.00 3.16
822 2390 0.588252 CAGCACGAGGAACAAACTGG 59.412 55.000 0.00 0.00 0.00 4.00
823 2391 0.535102 AGCACGAGGAACAAACTGGG 60.535 55.000 0.00 0.00 0.00 4.45
824 2392 0.818040 GCACGAGGAACAAACTGGGT 60.818 55.000 0.00 0.00 0.00 4.51
825 2393 1.541670 GCACGAGGAACAAACTGGGTA 60.542 52.381 0.00 0.00 0.00 3.69
826 2394 2.874457 GCACGAGGAACAAACTGGGTAT 60.874 50.000 0.00 0.00 0.00 2.73
827 2395 3.618019 GCACGAGGAACAAACTGGGTATA 60.618 47.826 0.00 0.00 0.00 1.47
828 2396 4.766375 CACGAGGAACAAACTGGGTATAT 58.234 43.478 0.00 0.00 0.00 0.86
829 2397 4.570772 CACGAGGAACAAACTGGGTATATG 59.429 45.833 0.00 0.00 0.00 1.78
830 2398 4.224370 ACGAGGAACAAACTGGGTATATGT 59.776 41.667 0.00 0.00 0.00 2.29
831 2399 4.809426 CGAGGAACAAACTGGGTATATGTC 59.191 45.833 0.00 0.00 0.00 3.06
832 2400 5.112129 AGGAACAAACTGGGTATATGTCC 57.888 43.478 0.00 0.00 0.00 4.02
833 2401 3.875134 GGAACAAACTGGGTATATGTCCG 59.125 47.826 0.00 0.00 0.00 4.79
834 2402 2.914059 ACAAACTGGGTATATGTCCGC 58.086 47.619 0.00 0.00 0.00 5.54
964 2532 0.547075 AGGAGATCCCGACGAGAAGA 59.453 55.000 0.00 0.00 40.87 2.87
1340 2908 2.586079 CGCGTCCGCCTGATCAAT 60.586 61.111 6.04 0.00 37.98 2.57
1361 2929 1.291877 CGGTTCCTGCTCCTGTTTCG 61.292 60.000 0.00 0.00 0.00 3.46
1616 3184 8.709308 AGAACTAGTAGACCAATTATGCATCTT 58.291 33.333 0.19 0.00 0.00 2.40
1707 3278 2.632996 AGAACTGGATGTTTCTGTCGGA 59.367 45.455 0.00 0.00 39.30 4.55
1725 3296 5.245977 TGTCGGATAATTAGGCATCTCATGA 59.754 40.000 0.00 0.00 0.00 3.07
1728 3299 7.010923 GTCGGATAATTAGGCATCTCATGATTC 59.989 40.741 0.00 0.00 0.00 2.52
1831 3403 4.319046 GCTATGCCATGTTCATAACACTCG 60.319 45.833 0.00 0.00 45.50 4.18
1877 3449 3.784178 TGATGGCCTTTTATGGTGGAAA 58.216 40.909 3.32 0.00 0.00 3.13
2002 3575 7.848051 CAGAACTTTAGCTATGCAATCTAAACG 59.152 37.037 11.81 10.86 31.40 3.60
2145 3718 4.542697 AGAGAAAACCTAGAGGCTAGAGG 58.457 47.826 11.69 11.69 39.32 3.69
2160 3733 2.831685 AGAGGTTGTGCGATGTAACA 57.168 45.000 0.00 0.00 0.00 2.41
2170 3743 2.287308 TGCGATGTAACAAACTGGCAAC 60.287 45.455 0.00 0.00 0.00 4.17
2184 3757 3.932545 TGGCAACATAATTGGTGTGTC 57.067 42.857 0.00 0.00 46.17 3.67
2185 3758 3.495331 TGGCAACATAATTGGTGTGTCT 58.505 40.909 0.00 0.00 46.17 3.41
2186 3759 4.657013 TGGCAACATAATTGGTGTGTCTA 58.343 39.130 0.00 0.00 46.17 2.59
2187 3760 4.699735 TGGCAACATAATTGGTGTGTCTAG 59.300 41.667 0.00 0.00 46.17 2.43
2188 3761 4.096382 GGCAACATAATTGGTGTGTCTAGG 59.904 45.833 0.00 0.00 42.86 3.02
2189 3762 4.096382 GCAACATAATTGGTGTGTCTAGGG 59.904 45.833 0.00 0.00 42.86 3.53
2190 3763 3.886123 ACATAATTGGTGTGTCTAGGGC 58.114 45.455 0.00 0.00 0.00 5.19
2191 3764 3.265737 ACATAATTGGTGTGTCTAGGGCA 59.734 43.478 0.00 0.00 0.00 5.36
2192 3765 2.200373 AATTGGTGTGTCTAGGGCAC 57.800 50.000 10.20 10.20 37.37 5.01
2193 3766 1.064003 ATTGGTGTGTCTAGGGCACA 58.936 50.000 14.22 14.22 43.60 4.57
2194 3767 1.064003 TTGGTGTGTCTAGGGCACAT 58.936 50.000 18.92 0.00 46.66 3.21
2195 3768 0.613260 TGGTGTGTCTAGGGCACATC 59.387 55.000 18.92 18.69 46.66 3.06
2196 3769 0.107654 GGTGTGTCTAGGGCACATCC 60.108 60.000 18.92 17.20 46.66 3.51
2197 3770 0.613260 GTGTGTCTAGGGCACATCCA 59.387 55.000 18.92 0.00 46.66 3.41
2198 3771 0.904649 TGTGTCTAGGGCACATCCAG 59.095 55.000 14.22 0.00 41.32 3.86
2199 3772 1.195115 GTGTCTAGGGCACATCCAGA 58.805 55.000 11.67 0.00 36.88 3.86
2200 3773 1.765314 GTGTCTAGGGCACATCCAGAT 59.235 52.381 11.67 0.00 36.88 2.90
2201 3774 1.764723 TGTCTAGGGCACATCCAGATG 59.235 52.381 6.09 6.09 44.15 2.90
2217 3790 8.437360 CATCCAGATGTACTTTAGTTATTGCA 57.563 34.615 0.00 0.00 34.23 4.08
2218 3791 7.843490 TCCAGATGTACTTTAGTTATTGCAC 57.157 36.000 0.00 0.00 0.00 4.57
2219 3792 7.390823 TCCAGATGTACTTTAGTTATTGCACA 58.609 34.615 0.00 0.00 0.00 4.57
2220 3793 8.046708 TCCAGATGTACTTTAGTTATTGCACAT 58.953 33.333 0.00 0.00 0.00 3.21
2221 3794 8.338259 CCAGATGTACTTTAGTTATTGCACATC 58.662 37.037 10.88 10.88 40.69 3.06
2226 3799 9.938280 TGTACTTTAGTTATTGCACATCTAAGT 57.062 29.630 0.00 0.00 0.00 2.24
2229 3802 9.155975 ACTTTAGTTATTGCACATCTAAGTGAG 57.844 33.333 0.00 0.00 42.05 3.51
2230 3803 9.155975 CTTTAGTTATTGCACATCTAAGTGAGT 57.844 33.333 0.00 0.00 42.05 3.41
2231 3804 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
2232 3805 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
2233 3806 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
2234 3807 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
2235 3808 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
2236 3809 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
2237 3810 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
2238 3811 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
2239 3812 5.641209 GCACATCTAAGTGAGTGAATCAAGT 59.359 40.000 0.00 0.00 42.05 3.16
2240 3813 6.813649 GCACATCTAAGTGAGTGAATCAAGTA 59.186 38.462 0.00 0.00 42.05 2.24
2241 3814 7.493971 GCACATCTAAGTGAGTGAATCAAGTAT 59.506 37.037 0.00 0.00 42.05 2.12
2279 3852 7.644986 AAGAGAGAAAGAAAGTATTCACACG 57.355 36.000 0.00 0.00 38.06 4.49
2280 3853 6.982852 AGAGAGAAAGAAAGTATTCACACGA 58.017 36.000 0.00 0.00 38.06 4.35
2281 3854 7.434492 AGAGAGAAAGAAAGTATTCACACGAA 58.566 34.615 0.00 0.00 38.06 3.85
2282 3855 8.091449 AGAGAGAAAGAAAGTATTCACACGAAT 58.909 33.333 0.00 0.00 44.24 3.34
2283 3856 8.245701 AGAGAAAGAAAGTATTCACACGAATC 57.754 34.615 0.00 0.00 41.09 2.52
2284 3857 8.091449 AGAGAAAGAAAGTATTCACACGAATCT 58.909 33.333 0.00 0.00 41.09 2.40
2285 3858 8.608844 AGAAAGAAAGTATTCACACGAATCTT 57.391 30.769 0.00 0.00 41.09 2.40
2286 3859 9.706691 AGAAAGAAAGTATTCACACGAATCTTA 57.293 29.630 0.00 0.00 41.09 2.10
2290 3863 9.436957 AGAAAGTATTCACACGAATCTTAATGT 57.563 29.630 0.00 0.00 41.09 2.71
2331 3904 8.818141 TGACTTAGATGTGCAATACTTATAGC 57.182 34.615 0.00 0.00 0.00 2.97
2332 3905 8.421002 TGACTTAGATGTGCAATACTTATAGCA 58.579 33.333 0.00 0.00 34.10 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.859411 AACAAGTTTGGCGAGAACAAA 57.141 38.095 0.00 0.00 35.62 2.83
48 49 7.725844 AGAGGGAATTCATAGTCAAACAAGTTT 59.274 33.333 7.93 0.00 0.00 2.66
55 56 5.339200 GGGTCAGAGGGAATTCATAGTCAAA 60.339 44.000 7.93 0.00 0.00 2.69
64 65 2.840651 TCTTCAGGGTCAGAGGGAATTC 59.159 50.000 0.00 0.00 0.00 2.17
103 104 6.117975 TCTGCATACATGATGATGGTACAT 57.882 37.500 0.00 0.00 38.64 2.29
106 107 6.013984 ACAGATCTGCATACATGATGATGGTA 60.014 38.462 22.83 0.00 37.82 3.25
112 113 6.224584 AGAGAACAGATCTGCATACATGATG 58.775 40.000 22.83 0.00 38.96 3.07
128 129 0.969894 ACCGAACAGGGAGAGAACAG 59.030 55.000 0.00 0.00 46.96 3.16
140 141 2.163818 GTCAAGATGACCACCGAACA 57.836 50.000 0.00 0.00 41.37 3.18
152 153 6.152323 CCAGATTGTTCAGAATTGGTCAAGAT 59.848 38.462 0.00 0.00 0.00 2.40
182 183 4.661222 TGGTCATCTTTGCCTATTGTGAA 58.339 39.130 0.00 0.00 0.00 3.18
222 223 1.508632 GAGTGTACGCTTGAAAGGCA 58.491 50.000 10.89 0.00 0.00 4.75
223 224 0.796927 GGAGTGTACGCTTGAAAGGC 59.203 55.000 10.89 0.00 0.00 4.35
228 229 0.535335 GGGATGGAGTGTACGCTTGA 59.465 55.000 10.89 0.46 0.00 3.02
232 233 0.178068 ATGTGGGATGGAGTGTACGC 59.822 55.000 0.00 0.00 0.00 4.42
261 265 8.714179 ACAAACAATCTTGCAAAACATCATATG 58.286 29.630 0.00 0.00 0.00 1.78
263 267 7.171167 CCACAAACAATCTTGCAAAACATCATA 59.829 33.333 0.00 0.00 0.00 2.15
287 291 2.379972 ACAAACGACAAAATCCCACCA 58.620 42.857 0.00 0.00 0.00 4.17
306 310 6.834876 AGAACCATTTTAATCGTCGGTTTAC 58.165 36.000 0.00 0.00 36.88 2.01
359 368 8.231837 GCACTTTCCGTACTATTGTATTCAAAA 58.768 33.333 0.00 0.00 37.11 2.44
362 371 6.636705 AGCACTTTCCGTACTATTGTATTCA 58.363 36.000 0.00 0.00 0.00 2.57
369 378 5.185249 TCTCTGAAGCACTTTCCGTACTATT 59.815 40.000 0.00 0.00 34.77 1.73
376 385 2.872245 TGTTTCTCTGAAGCACTTTCCG 59.128 45.455 0.00 0.00 34.77 4.30
379 388 6.866480 TCAAATTGTTTCTCTGAAGCACTTT 58.134 32.000 6.64 6.64 0.00 2.66
412 421 7.406031 TCGTCAGATAGGATTTTTGTACTCT 57.594 36.000 0.00 0.00 0.00 3.24
413 422 7.113684 CGATCGTCAGATAGGATTTTTGTACTC 59.886 40.741 7.03 0.00 37.19 2.59
414 423 6.918569 CGATCGTCAGATAGGATTTTTGTACT 59.081 38.462 7.03 0.00 37.19 2.73
420 429 5.006746 GCAAACGATCGTCAGATAGGATTTT 59.993 40.000 22.98 4.32 37.19 1.82
433 442 1.405821 CCTCTCCTAGCAAACGATCGT 59.594 52.381 16.60 16.60 0.00 3.73
437 446 0.252103 ACCCCTCTCCTAGCAAACGA 60.252 55.000 0.00 0.00 0.00 3.85
541 550 5.237815 TCTTCATAGCGACATGACAGTTTT 58.762 37.500 0.00 0.00 34.69 2.43
558 567 3.808618 GCGAGGGATGGCTATTTCTTCAT 60.809 47.826 0.00 0.00 0.00 2.57
559 568 2.485479 GCGAGGGATGGCTATTTCTTCA 60.485 50.000 0.00 0.00 0.00 3.02
560 569 2.147150 GCGAGGGATGGCTATTTCTTC 58.853 52.381 0.00 0.00 0.00 2.87
567 576 0.397957 TTAGGTGCGAGGGATGGCTA 60.398 55.000 0.00 0.00 0.00 3.93
596 605 3.551863 GGTGGCGTTTGTGAATGATTTCA 60.552 43.478 0.00 0.00 39.54 2.69
612 621 4.561735 TTGTTAAAAGAAGAAGGTGGCG 57.438 40.909 0.00 0.00 0.00 5.69
619 628 6.022821 CGGTGAACGTTTGTTAAAAGAAGAA 58.977 36.000 0.46 0.00 38.78 2.52
620 629 5.447548 CCGGTGAACGTTTGTTAAAAGAAGA 60.448 40.000 0.46 0.00 42.24 2.87
621 630 4.731480 CCGGTGAACGTTTGTTAAAAGAAG 59.269 41.667 0.46 0.00 42.24 2.85
623 632 3.487209 GCCGGTGAACGTTTGTTAAAAGA 60.487 43.478 0.46 0.00 42.24 2.52
625 634 2.422832 AGCCGGTGAACGTTTGTTAAAA 59.577 40.909 0.46 0.00 42.24 1.52
626 635 2.015587 AGCCGGTGAACGTTTGTTAAA 58.984 42.857 0.46 0.00 42.24 1.52
627 636 1.666054 AGCCGGTGAACGTTTGTTAA 58.334 45.000 0.46 0.00 42.24 2.01
630 639 1.223187 CTTAGCCGGTGAACGTTTGT 58.777 50.000 0.46 0.00 42.24 2.83
636 645 0.958876 CAACCCCTTAGCCGGTGAAC 60.959 60.000 1.90 0.00 30.96 3.18
654 2191 6.015772 GGACAATTAACCTGGCTTACTTTTCA 60.016 38.462 0.00 0.00 0.00 2.69
655 2192 6.015772 TGGACAATTAACCTGGCTTACTTTTC 60.016 38.462 0.00 0.00 0.00 2.29
668 2205 6.635030 AGTTTCTTCACTGGACAATTAACC 57.365 37.500 0.00 0.00 0.00 2.85
671 2208 7.963532 ACTCTAGTTTCTTCACTGGACAATTA 58.036 34.615 0.00 0.00 31.48 1.40
672 2209 6.831976 ACTCTAGTTTCTTCACTGGACAATT 58.168 36.000 0.00 0.00 31.48 2.32
706 2246 6.417044 CCTCGTATCCTTTTGTTGTACTATCG 59.583 42.308 0.00 0.00 0.00 2.92
710 2250 4.323257 CCCCTCGTATCCTTTTGTTGTACT 60.323 45.833 0.00 0.00 0.00 2.73
712 2252 3.054948 CCCCCTCGTATCCTTTTGTTGTA 60.055 47.826 0.00 0.00 0.00 2.41
807 2375 4.224370 ACATATACCCAGTTTGTTCCTCGT 59.776 41.667 0.00 0.00 0.00 4.18
808 2376 4.766375 ACATATACCCAGTTTGTTCCTCG 58.234 43.478 0.00 0.00 0.00 4.63
809 2377 5.123936 GGACATATACCCAGTTTGTTCCTC 58.876 45.833 0.00 0.00 0.00 3.71
810 2378 4.383770 CGGACATATACCCAGTTTGTTCCT 60.384 45.833 0.00 0.00 0.00 3.36
811 2379 3.875134 CGGACATATACCCAGTTTGTTCC 59.125 47.826 0.00 0.00 0.00 3.62
812 2380 3.311596 GCGGACATATACCCAGTTTGTTC 59.688 47.826 0.00 0.00 0.00 3.18
813 2381 3.054655 AGCGGACATATACCCAGTTTGTT 60.055 43.478 0.00 0.00 0.00 2.83
814 2382 2.504175 AGCGGACATATACCCAGTTTGT 59.496 45.455 0.00 0.00 0.00 2.83
815 2383 3.131396 GAGCGGACATATACCCAGTTTG 58.869 50.000 0.00 0.00 0.00 2.93
816 2384 2.769663 TGAGCGGACATATACCCAGTTT 59.230 45.455 0.00 0.00 0.00 2.66
817 2385 2.102588 GTGAGCGGACATATACCCAGTT 59.897 50.000 0.00 0.00 0.00 3.16
818 2386 1.687123 GTGAGCGGACATATACCCAGT 59.313 52.381 0.00 0.00 0.00 4.00
819 2387 1.964223 AGTGAGCGGACATATACCCAG 59.036 52.381 0.00 0.00 0.00 4.45
820 2388 1.686587 CAGTGAGCGGACATATACCCA 59.313 52.381 0.00 0.00 0.00 4.51
821 2389 1.961394 TCAGTGAGCGGACATATACCC 59.039 52.381 0.00 0.00 0.00 3.69
822 2390 2.288273 GGTCAGTGAGCGGACATATACC 60.288 54.545 6.57 0.00 40.75 2.73
823 2391 3.014604 GGTCAGTGAGCGGACATATAC 57.985 52.381 6.57 0.00 40.75 1.47
834 2402 4.394712 GGCCCACCGGTCAGTGAG 62.395 72.222 2.59 0.00 40.34 3.51
1170 2738 0.895100 GCAGCATGTTGTTCCCTCCA 60.895 55.000 11.44 0.00 39.31 3.86
1340 2908 1.415672 AAACAGGAGCAGGAACCGGA 61.416 55.000 9.46 0.00 0.00 5.14
1361 2929 4.574421 TCTGATCTGATCTGAGACGAAGAC 59.426 45.833 19.44 0.00 33.94 3.01
1587 3155 7.847096 TGCATAATTGGTCTACTAGTTCTCAA 58.153 34.615 0.00 2.05 0.00 3.02
1616 3184 2.672961 AGCAACGTATGAAGCTAGCA 57.327 45.000 18.83 0.00 35.19 3.49
1725 3296 4.241681 GACACAGAAGCTCGAGAAAGAAT 58.758 43.478 18.75 0.00 0.00 2.40
1728 3299 2.728839 GTGACACAGAAGCTCGAGAAAG 59.271 50.000 18.75 2.89 0.00 2.62
1809 3380 5.049828 TCGAGTGTTATGAACATGGCATAG 58.950 41.667 0.00 0.00 44.35 2.23
1831 3403 3.924686 CCATGAAAACAGCAGAGCATTTC 59.075 43.478 0.00 0.00 32.60 2.17
1877 3449 5.047519 CCCTGTCAAAAGATTGAGCAGAATT 60.048 40.000 15.96 0.00 45.88 2.17
1958 3530 6.278363 AGTTCTGTCTTACACGTTACAACAT 58.722 36.000 0.00 0.00 0.00 2.71
2002 3575 1.404843 TTTGCCCAAAGTACCACCAC 58.595 50.000 0.00 0.00 0.00 4.16
2054 3627 7.835682 TCAACAATCCAAGGTTCAGATCAATAT 59.164 33.333 0.00 0.00 0.00 1.28
2145 3718 3.296628 CCAGTTTGTTACATCGCACAAC 58.703 45.455 0.00 0.00 32.57 3.32
2160 3733 4.100808 ACACACCAATTATGTTGCCAGTTT 59.899 37.500 0.00 0.00 0.00 2.66
2170 3743 3.627577 GTGCCCTAGACACACCAATTATG 59.372 47.826 10.07 0.00 37.96 1.90
2180 3753 1.195115 TCTGGATGTGCCCTAGACAC 58.805 55.000 8.47 8.47 38.55 3.67
2181 3754 1.764723 CATCTGGATGTGCCCTAGACA 59.235 52.381 2.69 0.00 34.23 3.41
2182 3755 2.540265 CATCTGGATGTGCCCTAGAC 57.460 55.000 2.69 0.00 34.23 2.59
2192 3765 8.338259 GTGCAATAACTAAAGTACATCTGGATG 58.662 37.037 8.81 8.81 44.15 3.51
2193 3766 8.046708 TGTGCAATAACTAAAGTACATCTGGAT 58.953 33.333 0.00 0.00 0.00 3.41
2194 3767 7.390823 TGTGCAATAACTAAAGTACATCTGGA 58.609 34.615 0.00 0.00 0.00 3.86
2195 3768 7.609760 TGTGCAATAACTAAAGTACATCTGG 57.390 36.000 0.00 0.00 0.00 3.86
2200 3773 9.938280 ACTTAGATGTGCAATAACTAAAGTACA 57.062 29.630 0.00 0.00 0.00 2.90
2203 3776 9.155975 CTCACTTAGATGTGCAATAACTAAAGT 57.844 33.333 0.00 0.00 37.81 2.66
2204 3777 9.155975 ACTCACTTAGATGTGCAATAACTAAAG 57.844 33.333 0.00 0.00 37.81 1.85
2205 3778 8.935844 CACTCACTTAGATGTGCAATAACTAAA 58.064 33.333 0.00 0.00 37.81 1.85
2206 3779 8.311109 TCACTCACTTAGATGTGCAATAACTAA 58.689 33.333 0.00 0.00 37.81 2.24
2207 3780 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
2208 3781 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
2209 3782 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
2210 3783 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
2211 3784 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
2212 3785 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
2213 3786 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
2214 3787 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
2215 3788 5.641209 ACTTGATTCACTCACTTAGATGTGC 59.359 40.000 0.00 0.00 37.81 4.57
2216 3789 8.939201 ATACTTGATTCACTCACTTAGATGTG 57.061 34.615 0.00 0.00 39.15 3.21
2253 3826 8.552034 CGTGTGAATACTTTCTTTCTCTCTTTT 58.448 33.333 0.00 0.00 32.78 2.27
2254 3827 7.926555 TCGTGTGAATACTTTCTTTCTCTCTTT 59.073 33.333 0.00 0.00 32.78 2.52
2255 3828 7.434492 TCGTGTGAATACTTTCTTTCTCTCTT 58.566 34.615 0.00 0.00 32.78 2.85
2256 3829 6.982852 TCGTGTGAATACTTTCTTTCTCTCT 58.017 36.000 0.00 0.00 32.78 3.10
2257 3830 7.639162 TTCGTGTGAATACTTTCTTTCTCTC 57.361 36.000 0.00 0.00 32.78 3.20
2258 3831 8.091449 AGATTCGTGTGAATACTTTCTTTCTCT 58.909 33.333 0.00 0.00 44.79 3.10
2259 3832 8.245701 AGATTCGTGTGAATACTTTCTTTCTC 57.754 34.615 0.00 0.00 44.79 2.87
2260 3833 8.608844 AAGATTCGTGTGAATACTTTCTTTCT 57.391 30.769 0.00 0.00 44.79 2.52
2264 3837 9.436957 ACATTAAGATTCGTGTGAATACTTTCT 57.563 29.630 0.00 0.00 44.79 2.52
2305 3878 9.429359 GCTATAAGTATTGCACATCTAAGTCAT 57.571 33.333 0.00 0.00 35.12 3.06
2306 3879 8.421002 TGCTATAAGTATTGCACATCTAAGTCA 58.579 33.333 3.73 0.00 38.99 3.41
2307 3880 8.818141 TGCTATAAGTATTGCACATCTAAGTC 57.182 34.615 3.73 0.00 38.99 3.01


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

AutoCloner maintained by Alex Coulton.