Multiple sequence alignment - TraesCS1A01G311100

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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 TraesCS1A01G311100 chr1A 100.000 3656 0 0 1 3656 502807511 502803856 0.000000e+00 6752.0
1 TraesCS1A01G311100 chr1A 94.595 37 2 0 2314 2350 544391486 544391522 1.420000e-04 58.4
2 TraesCS1A01G311100 chr1B 90.831 3741 198 67 1 3649 547525726 547522039 0.000000e+00 4874.0
3 TraesCS1A01G311100 chr1B 94.595 37 2 0 2314 2350 614506740 614506776 1.420000e-04 58.4
4 TraesCS1A01G311100 chr1D 90.139 3448 178 63 1 3366 407162683 407159316 0.000000e+00 4335.0
5 TraesCS1A01G311100 chr1D 85.802 324 33 7 3346 3656 407159302 407158979 7.570000e-87 331.0
6 TraesCS1A01G311100 chr1D 94.595 37 2 0 2314 2350 448788663 448788699 1.420000e-04 58.4
7 TraesCS1A01G311100 chr7D 83.537 164 27 0 1767 1930 417357560 417357397 1.760000e-33 154.0
8 TraesCS1A01G311100 chr7D 84.746 59 9 0 3400 3458 38107093 38107151 3.940000e-05 60.2
9 TraesCS1A01G311100 chr7B 82.738 168 29 0 1767 1934 433064154 433063987 2.270000e-32 150.0
10 TraesCS1A01G311100 chr7A 82.317 164 29 0 1767 1930 482217921 482217758 3.810000e-30 143.0
11 TraesCS1A01G311100 chr7A 88.750 80 6 3 3400 3477 232342957 232343035 1.080000e-15 95.3
12 TraesCS1A01G311100 chr7A 84.146 82 3 2 3091 3162 19371025 19370944 1.820000e-08 71.3
13 TraesCS1A01G311100 chr4A 86.301 73 8 2 3422 3494 703537683 703537753 1.090000e-10 78.7
14 TraesCS1A01G311100 chr4B 78.676 136 12 9 3041 3162 22551618 22551486 1.410000e-09 75.0
15 TraesCS1A01G311100 chr4B 85.507 69 9 1 3424 3492 59416650 59416583 1.820000e-08 71.3
16 TraesCS1A01G311100 chr5D 97.500 40 1 0 3123 3162 502366283 502366244 6.550000e-08 69.4
17 TraesCS1A01G311100 chr4D 88.136 59 5 2 3400 3458 497237419 497237475 6.550000e-08 69.4
18 TraesCS1A01G311100 chr4D 95.000 40 2 0 3123 3162 499592281 499592320 3.050000e-06 63.9
19 TraesCS1A01G311100 chr6D 95.000 40 2 0 3123 3162 47815133 47815094 3.050000e-06 63.9
20 TraesCS1A01G311100 chr5B 95.000 40 2 0 3123 3162 612083322 612083361 3.050000e-06 63.9
21 TraesCS1A01G311100 chr5A 77.037 135 16 8 3041 3162 636287715 636287847 3.050000e-06 63.9
22 TraesCS1A01G311100 chr2A 74.497 149 32 4 1896 2041 661082874 661083019 3.940000e-05 60.2


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 TraesCS1A01G311100 chr1A 502803856 502807511 3655 True 6752 6752 100.0000 1 3656 1 chr1A.!!$R1 3655
1 TraesCS1A01G311100 chr1B 547522039 547525726 3687 True 4874 4874 90.8310 1 3649 1 chr1B.!!$R1 3648
2 TraesCS1A01G311100 chr1D 407158979 407162683 3704 True 2333 4335 87.9705 1 3656 2 chr1D.!!$R1 3655

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
266 283 0.108329 GATCGCCGAAAAGTGGGAGA 60.108 55.0 0.00 0.00 35.96 3.71 F
1687 1726 0.108329 CCTAACCCAGCCACGTACTG 60.108 60.0 10.12 10.12 34.82 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1786 0.037326 TGCACAGGAGATCAACGTCC 60.037 55.0 0.0 0.0 0.0 4.79 R
3126 3228 0.107263 TTGCTGTTCTGGTGTGCTGA 60.107 50.0 0.0 0.0 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
19 20 1.087501 GTGCAAAAGGAGATCGGTCC 58.912 55.000 0.00 0.00 36.79 4.46
20 21 0.690192 TGCAAAAGGAGATCGGTCCA 59.310 50.000 3.98 0.00 39.34 4.02
96 97 6.018425 GGTCGTATCTCAGTTGTCGTAGATAA 60.018 42.308 0.00 0.00 40.67 1.75
97 98 7.064674 GTCGTATCTCAGTTGTCGTAGATAAG 58.935 42.308 0.00 0.00 38.57 1.73
98 99 6.982724 TCGTATCTCAGTTGTCGTAGATAAGA 59.017 38.462 0.00 0.00 38.57 2.10
99 100 7.169476 TCGTATCTCAGTTGTCGTAGATAAGAG 59.831 40.741 0.00 0.00 38.57 2.85
100 101 7.042590 CGTATCTCAGTTGTCGTAGATAAGAGT 60.043 40.741 0.00 0.00 38.57 3.24
101 102 9.258826 GTATCTCAGTTGTCGTAGATAAGAGTA 57.741 37.037 0.00 0.00 38.57 2.59
206 211 4.318949 GGGCAACGGTACCACGGT 62.319 66.667 13.54 0.00 38.39 4.83
212 223 0.530431 AACGGTACCACGGTTGTCAC 60.530 55.000 13.54 0.00 39.65 3.67
213 224 1.665599 CGGTACCACGGTTGTCACC 60.666 63.158 13.54 0.00 40.16 4.02
229 240 2.803670 CCGTGCACGTACGTCTGG 60.804 66.667 34.81 15.31 42.24 3.86
230 241 3.467119 CGTGCACGTACGTCTGGC 61.467 66.667 30.50 19.40 39.13 4.85
231 242 3.110178 GTGCACGTACGTCTGGCC 61.110 66.667 19.94 9.53 0.00 5.36
234 245 4.047059 CACGTACGTCTGGCCGGT 62.047 66.667 19.94 2.41 0.00 5.28
247 264 1.026718 GGCCGGTCTCATCAAGGTTG 61.027 60.000 1.90 0.00 0.00 3.77
262 279 0.168128 GGTTGATCGCCGAAAAGTGG 59.832 55.000 0.00 0.00 0.00 4.00
266 283 0.108329 GATCGCCGAAAAGTGGGAGA 60.108 55.000 0.00 0.00 35.96 3.71
330 359 1.831736 CCTACCCTGTCGTTCTTCCAT 59.168 52.381 0.00 0.00 0.00 3.41
338 367 3.996363 CTGTCGTTCTTCCATTGACATGA 59.004 43.478 0.00 0.00 38.72 3.07
339 368 3.745975 TGTCGTTCTTCCATTGACATGAC 59.254 43.478 0.00 0.00 34.85 3.06
340 369 3.125316 GTCGTTCTTCCATTGACATGACC 59.875 47.826 0.00 0.00 31.07 4.02
341 370 2.420022 CGTTCTTCCATTGACATGACCC 59.580 50.000 0.00 0.00 31.07 4.46
342 371 3.420893 GTTCTTCCATTGACATGACCCA 58.579 45.455 0.00 0.00 31.07 4.51
343 372 4.019174 GTTCTTCCATTGACATGACCCAT 58.981 43.478 0.00 0.00 31.07 4.00
344 373 5.192927 GTTCTTCCATTGACATGACCCATA 58.807 41.667 0.00 0.00 31.07 2.74
345 374 5.651612 TCTTCCATTGACATGACCCATAT 57.348 39.130 0.00 0.00 31.07 1.78
346 375 5.379187 TCTTCCATTGACATGACCCATATG 58.621 41.667 0.00 0.00 31.07 1.78
348 377 5.385628 TCCATTGACATGACCCATATGAA 57.614 39.130 3.65 0.00 31.07 2.57
350 379 6.193504 TCCATTGACATGACCCATATGAAAA 58.806 36.000 3.65 0.00 31.07 2.29
352 381 6.097270 CCATTGACATGACCCATATGAAAACT 59.903 38.462 3.65 0.00 31.07 2.66
354 383 4.949238 TGACATGACCCATATGAAAACTGG 59.051 41.667 3.65 0.00 0.00 4.00
355 384 4.934356 ACATGACCCATATGAAAACTGGT 58.066 39.130 3.65 1.15 0.00 4.00
356 385 5.332743 ACATGACCCATATGAAAACTGGTT 58.667 37.500 3.65 0.00 0.00 3.67
358 387 4.991776 TGACCCATATGAAAACTGGTTCA 58.008 39.130 3.65 0.51 41.59 3.18
361 390 5.332743 ACCCATATGAAAACTGGTTCACAT 58.667 37.500 3.65 1.83 40.22 3.21
362 391 5.185635 ACCCATATGAAAACTGGTTCACATG 59.814 40.000 3.65 7.32 40.54 3.21
363 392 5.185635 CCCATATGAAAACTGGTTCACATGT 59.814 40.000 3.65 0.00 39.66 3.21
364 393 6.324819 CCATATGAAAACTGGTTCACATGTC 58.675 40.000 3.65 0.00 39.66 3.06
365 394 6.072008 CCATATGAAAACTGGTTCACATGTCA 60.072 38.462 3.65 0.00 39.66 3.58
366 395 4.630894 TGAAAACTGGTTCACATGTCAC 57.369 40.909 0.00 0.00 32.56 3.67
367 396 4.269183 TGAAAACTGGTTCACATGTCACT 58.731 39.130 0.00 0.00 32.56 3.41
370 399 1.202806 ACTGGTTCACATGTCACTGGG 60.203 52.381 0.00 0.00 0.00 4.45
453 482 6.183360 TGCACTCAAAATTTTGCTTCTTTTCC 60.183 34.615 23.36 7.31 38.05 3.13
475 504 5.072329 TCCATTCAAAGATAGGGTGATCCTC 59.928 44.000 0.00 0.00 44.06 3.71
476 505 5.072872 CCATTCAAAGATAGGGTGATCCTCT 59.927 44.000 0.00 0.00 44.06 3.69
477 506 5.878406 TTCAAAGATAGGGTGATCCTCTC 57.122 43.478 0.00 0.00 44.06 3.20
589 619 3.378112 TGGAAATCGGTTTGCAGATCATC 59.622 43.478 11.66 0.00 40.19 2.92
590 620 3.546815 GGAAATCGGTTTGCAGATCATCG 60.547 47.826 7.89 0.00 35.90 3.84
610 640 3.620428 CGTGCATGGTAGCGAGCG 61.620 66.667 0.00 0.00 37.31 5.03
630 664 1.149854 AAGTCCAACCACGAACCCC 59.850 57.895 0.00 0.00 0.00 4.95
753 787 3.684788 GCCAGCCTATAAATCCATGTACG 59.315 47.826 0.00 0.00 0.00 3.67
804 838 2.175202 CACTAACTGTCCAGCTCCTCT 58.825 52.381 0.00 0.00 0.00 3.69
805 839 2.094286 CACTAACTGTCCAGCTCCTCTG 60.094 54.545 0.00 0.00 42.49 3.35
806 840 0.898320 TAACTGTCCAGCTCCTCTGC 59.102 55.000 0.00 0.00 41.50 4.26
807 841 0.835543 AACTGTCCAGCTCCTCTGCT 60.836 55.000 0.00 0.00 45.18 4.24
808 842 1.257055 ACTGTCCAGCTCCTCTGCTC 61.257 60.000 0.00 0.00 41.98 4.26
809 843 1.228988 TGTCCAGCTCCTCTGCTCA 60.229 57.895 0.00 0.00 41.98 4.26
827 861 4.520874 TGCTCATCTACTCCAGTATAGCAC 59.479 45.833 0.00 0.00 32.32 4.40
878 912 4.933064 CCGGGACAGCGCTCGATC 62.933 72.222 16.77 10.57 0.00 3.69
904 938 4.475135 GCCTTCCTCTGGGCGTCC 62.475 72.222 0.00 0.00 38.91 4.79
920 954 2.906354 CGTCCATATATAAGCAGGCCC 58.094 52.381 0.00 0.00 0.00 5.80
936 970 1.270358 GGCCCAGTGATCCGAGATTAC 60.270 57.143 0.00 0.00 0.00 1.89
956 990 3.113824 ACTCCATCCTTGAGCTGAATCT 58.886 45.455 0.00 0.00 32.98 2.40
959 993 5.028549 TCCATCCTTGAGCTGAATCTAAC 57.971 43.478 0.00 0.00 0.00 2.34
961 995 4.384537 CCATCCTTGAGCTGAATCTAACCA 60.385 45.833 0.00 0.00 0.00 3.67
963 997 4.579869 TCCTTGAGCTGAATCTAACCAAC 58.420 43.478 0.00 0.00 0.00 3.77
964 998 3.372206 CCTTGAGCTGAATCTAACCAACG 59.628 47.826 0.00 0.00 0.00 4.10
966 1000 1.324736 GAGCTGAATCTAACCAACGCG 59.675 52.381 3.53 3.53 0.00 6.01
968 1002 1.324736 GCTGAATCTAACCAACGCGAG 59.675 52.381 15.93 4.40 0.00 5.03
969 1003 1.324736 CTGAATCTAACCAACGCGAGC 59.675 52.381 15.93 0.00 0.00 5.03
970 1004 1.337354 TGAATCTAACCAACGCGAGCA 60.337 47.619 15.93 0.00 0.00 4.26
972 1006 1.359848 ATCTAACCAACGCGAGCAAG 58.640 50.000 15.93 2.12 0.00 4.01
1182 1221 1.115467 CTAAGCATGGGTCTCCGTCT 58.885 55.000 0.00 0.00 35.24 4.18
1185 1224 2.981302 CATGGGTCTCCGTCTGCA 59.019 61.111 0.00 0.00 35.24 4.41
1188 1227 3.311110 GGGTCTCCGTCTGCACCA 61.311 66.667 0.00 0.00 0.00 4.17
1587 1626 2.892425 CTCATCGACGGCAAGGGC 60.892 66.667 0.00 0.00 40.13 5.19
1687 1726 0.108329 CCTAACCCAGCCACGTACTG 60.108 60.000 10.12 10.12 34.82 2.74
1696 1739 1.630244 GCCACGTACTGCTGCTTCAG 61.630 60.000 0.00 4.59 39.86 3.02
1733 1780 6.902771 TTTTTAATGGCCAGTAAGTGCTAA 57.097 33.333 23.44 13.23 0.00 3.09
1735 1782 5.890424 TTAATGGCCAGTAAGTGCTAAAC 57.110 39.130 21.23 0.00 0.00 2.01
1736 1783 1.803334 TGGCCAGTAAGTGCTAAACG 58.197 50.000 0.00 0.00 0.00 3.60
1737 1784 0.446616 GGCCAGTAAGTGCTAAACGC 59.553 55.000 0.00 0.00 39.77 4.84
1739 1786 0.719465 CCAGTAAGTGCTAAACGCCG 59.281 55.000 0.00 0.00 38.05 6.46
1754 1801 1.519455 GCCGGACGTTGATCTCCTG 60.519 63.158 5.05 0.00 0.00 3.86
1756 1803 0.458543 CCGGACGTTGATCTCCTGTG 60.459 60.000 0.00 0.00 0.00 3.66
1807 1854 3.240134 GACGGTGCAAGGGCTCAGA 62.240 63.158 0.00 0.00 41.91 3.27
1879 1926 1.251527 ACGTCGACAGCCTCTCCATT 61.252 55.000 17.16 0.00 0.00 3.16
1939 1986 1.372997 CGAGAACACCCAGGACGTG 60.373 63.158 0.00 0.00 37.26 4.49
2061 2108 1.718757 GGCATCAGGTTCGCATCCAC 61.719 60.000 0.00 0.00 0.00 4.02
2088 2135 1.912110 CCTCGTCGTAGCTTTTCTTCG 59.088 52.381 0.00 0.00 37.00 3.79
2111 2158 6.541278 TCGGATGTTATATATACTCCACTCCG 59.459 42.308 16.84 16.84 41.45 4.63
2138 2189 2.401766 GCCTGACATTGGGTGCTCG 61.402 63.158 0.00 0.00 0.00 5.03
2140 2191 1.376424 CTGACATTGGGTGCTCGCT 60.376 57.895 4.41 0.00 0.00 4.93
2141 2192 1.364626 CTGACATTGGGTGCTCGCTC 61.365 60.000 4.41 0.00 0.00 5.03
2142 2193 1.078848 GACATTGGGTGCTCGCTCT 60.079 57.895 4.41 0.00 0.00 4.09
2143 2194 1.078848 ACATTGGGTGCTCGCTCTC 60.079 57.895 4.41 0.00 0.00 3.20
2144 2195 2.169789 CATTGGGTGCTCGCTCTCG 61.170 63.158 4.41 0.00 0.00 4.04
2145 2196 2.650116 ATTGGGTGCTCGCTCTCGT 61.650 57.895 4.41 0.00 36.96 4.18
2146 2197 2.172483 ATTGGGTGCTCGCTCTCGTT 62.172 55.000 4.41 0.00 36.96 3.85
2166 2217 4.804420 AGCATCGGGAGCCTGGGA 62.804 66.667 0.00 0.00 0.00 4.37
2571 2622 2.025418 CGTCTACGGCAACACCACC 61.025 63.158 0.00 0.00 39.03 4.61
2631 2682 1.002624 GCCCAGGAACGTGGATGAA 60.003 57.895 14.02 0.00 40.44 2.57
2632 2683 1.026718 GCCCAGGAACGTGGATGAAG 61.027 60.000 14.02 0.00 40.44 3.02
2668 2719 2.030628 TGTTACTGATGAGCGACGTCAA 60.031 45.455 17.16 0.00 42.90 3.18
2692 2743 0.317160 TCGCACGCCCCTTATAGATG 59.683 55.000 0.00 0.00 0.00 2.90
2732 2786 7.454225 ACCAGAGAAAATATATTAGGCCAGAC 58.546 38.462 5.01 0.00 0.00 3.51
2761 2816 4.451096 ACTTAGTTAAAGCATGGTCGTGTG 59.549 41.667 0.00 0.00 38.93 3.82
2762 2817 2.846193 AGTTAAAGCATGGTCGTGTGT 58.154 42.857 0.00 0.00 0.00 3.72
2763 2818 3.997762 AGTTAAAGCATGGTCGTGTGTA 58.002 40.909 0.00 0.00 0.00 2.90
2764 2819 3.994392 AGTTAAAGCATGGTCGTGTGTAG 59.006 43.478 0.00 0.00 0.00 2.74
2766 2821 3.671008 AAAGCATGGTCGTGTGTAGTA 57.329 42.857 0.00 0.00 0.00 1.82
2767 2822 3.887621 AAGCATGGTCGTGTGTAGTAT 57.112 42.857 0.00 0.00 0.00 2.12
2768 2823 4.994907 AAGCATGGTCGTGTGTAGTATA 57.005 40.909 0.00 0.00 0.00 1.47
2769 2824 4.994907 AGCATGGTCGTGTGTAGTATAA 57.005 40.909 0.00 0.00 0.00 0.98
2825 2880 9.793252 AAAATGTAACAGTATGAGATGATTTGC 57.207 29.630 0.00 0.00 39.69 3.68
3063 3164 2.742372 GCACCGCCGTCATTGTCT 60.742 61.111 0.00 0.00 0.00 3.41
3081 3182 1.535444 TCCCTCTCACCGAAGCCAA 60.535 57.895 0.00 0.00 0.00 4.52
3087 3188 3.077359 CTCTCACCGAAGCCAAGAAAAT 58.923 45.455 0.00 0.00 0.00 1.82
3089 3190 4.647611 TCTCACCGAAGCCAAGAAAATTA 58.352 39.130 0.00 0.00 0.00 1.40
3126 3228 2.292016 CGAGAGTCGTCATGCTAAGGAT 59.708 50.000 0.00 0.00 34.72 3.24
3171 3273 1.005340 CAGATGAAGAGAAGTGGCGC 58.995 55.000 0.00 0.00 0.00 6.53
3172 3274 0.107945 AGATGAAGAGAAGTGGCGCC 60.108 55.000 22.73 22.73 0.00 6.53
3173 3275 1.424493 GATGAAGAGAAGTGGCGCCG 61.424 60.000 23.90 0.00 0.00 6.46
3177 3280 1.812686 AAGAGAAGTGGCGCCGTGTA 61.813 55.000 23.90 0.00 0.00 2.90
3186 3289 1.566018 GGCGCCGTGTATTCATAGGC 61.566 60.000 12.58 10.38 42.45 3.93
3241 3345 7.953173 CGCGTCTGTAATGTGTTTCTTAATTTA 59.047 33.333 0.00 0.00 0.00 1.40
3301 3405 3.547613 GCACATGAATCAGCTCGGAATTC 60.548 47.826 0.00 0.00 0.00 2.17
3310 3414 3.571828 TCAGCTCGGAATTCCATCTAGAG 59.428 47.826 24.09 20.29 35.14 2.43
3354 3458 4.439057 TGTGAAGTCTGTGAACAAGTACC 58.561 43.478 0.00 0.00 0.00 3.34
3357 3461 4.163458 TGAAGTCTGTGAACAAGTACCCTT 59.837 41.667 0.00 0.00 0.00 3.95
3385 3522 8.783093 TGGCTTTATGAAATCTATAATTCCGTG 58.217 33.333 0.00 0.00 0.00 4.94
3409 3546 2.173569 GTGGCCCTGAAAGATGGTCTAT 59.826 50.000 0.00 0.00 34.07 1.98
3423 3560 7.379059 AGATGGTCTATGGACATGAACATAA 57.621 36.000 11.67 0.00 43.77 1.90
3459 3600 3.146066 GTGTTCTTTGTACTGCCATGGA 58.854 45.455 18.40 0.00 0.00 3.41
3602 3744 3.310774 GCGCATCTCTGTCAACAATGTAT 59.689 43.478 0.30 0.00 0.00 2.29
3603 3745 4.201851 GCGCATCTCTGTCAACAATGTATT 60.202 41.667 0.30 0.00 0.00 1.89
3604 3746 5.496387 CGCATCTCTGTCAACAATGTATTC 58.504 41.667 0.00 0.00 0.00 1.75
3605 3747 5.063817 CGCATCTCTGTCAACAATGTATTCA 59.936 40.000 0.00 0.00 0.00 2.57
3606 3748 6.238293 CGCATCTCTGTCAACAATGTATTCAT 60.238 38.462 0.00 0.00 35.59 2.57
3607 3749 7.042523 CGCATCTCTGTCAACAATGTATTCATA 60.043 37.037 0.00 0.00 33.49 2.15
3608 3750 8.281194 GCATCTCTGTCAACAATGTATTCATAG 58.719 37.037 0.00 0.00 33.49 2.23
3609 3751 9.538508 CATCTCTGTCAACAATGTATTCATAGA 57.461 33.333 0.00 0.00 33.49 1.98
3610 3752 8.932945 TCTCTGTCAACAATGTATTCATAGAC 57.067 34.615 0.00 0.00 33.49 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 211 1.945169 CGTACGTGCACGGTGACAA 60.945 57.895 39.21 16.72 44.95 3.18
212 223 2.803670 CCAGACGTACGTGCACGG 60.804 66.667 39.21 25.48 46.12 4.94
229 240 0.036388 TCAACCTTGATGAGACCGGC 60.036 55.000 0.00 0.00 31.01 6.13
230 241 2.698855 ATCAACCTTGATGAGACCGG 57.301 50.000 0.00 0.00 45.63 5.28
247 264 0.108329 TCTCCCACTTTTCGGCGATC 60.108 55.000 11.76 0.00 0.00 3.69
319 348 3.334691 GGTCATGTCAATGGAAGAACGA 58.665 45.455 0.00 0.00 34.30 3.85
330 359 5.418524 CCAGTTTTCATATGGGTCATGTCAA 59.581 40.000 2.13 0.00 0.00 3.18
338 367 4.735369 TGTGAACCAGTTTTCATATGGGT 58.265 39.130 2.13 0.00 37.80 4.51
339 368 5.653507 CATGTGAACCAGTTTTCATATGGG 58.346 41.667 12.33 0.00 44.88 4.00
342 371 6.716628 AGTGACATGTGAACCAGTTTTCATAT 59.283 34.615 1.15 0.00 37.70 1.78
343 372 6.017192 CAGTGACATGTGAACCAGTTTTCATA 60.017 38.462 1.15 0.00 37.80 2.15
344 373 4.889409 AGTGACATGTGAACCAGTTTTCAT 59.111 37.500 1.15 0.00 37.80 2.57
345 374 4.096231 CAGTGACATGTGAACCAGTTTTCA 59.904 41.667 1.15 0.00 32.94 2.69
346 375 4.498009 CCAGTGACATGTGAACCAGTTTTC 60.498 45.833 1.15 0.00 0.00 2.29
348 377 2.951642 CCAGTGACATGTGAACCAGTTT 59.048 45.455 1.15 0.00 0.00 2.66
350 379 1.202806 CCCAGTGACATGTGAACCAGT 60.203 52.381 1.15 0.00 0.00 4.00
352 381 1.135960 TCCCAGTGACATGTGAACCA 58.864 50.000 1.15 0.00 0.00 3.67
362 391 1.146041 TGCTGTGTGTCCCAGTGAC 59.854 57.895 0.00 0.00 44.72 3.67
363 392 1.146041 GTGCTGTGTGTCCCAGTGA 59.854 57.895 0.00 0.00 32.41 3.41
364 393 2.246739 CGTGCTGTGTGTCCCAGTG 61.247 63.158 0.00 0.00 32.41 3.66
365 394 2.108976 CGTGCTGTGTGTCCCAGT 59.891 61.111 0.00 0.00 32.41 4.00
366 395 2.666190 CCGTGCTGTGTGTCCCAG 60.666 66.667 0.00 0.00 0.00 4.45
367 396 4.927782 GCCGTGCTGTGTGTCCCA 62.928 66.667 0.00 0.00 0.00 4.37
370 399 2.280119 TCTGCCGTGCTGTGTGTC 60.280 61.111 0.00 0.00 0.00 3.67
376 405 1.817099 GGATTCCTCTGCCGTGCTG 60.817 63.158 0.00 0.00 0.00 4.41
377 406 2.249413 CTGGATTCCTCTGCCGTGCT 62.249 60.000 3.95 0.00 0.00 4.40
475 504 8.662781 TGGTTTCTATTAATGGAAATCGAGAG 57.337 34.615 24.36 0.08 40.11 3.20
476 505 9.456147 TTTGGTTTCTATTAATGGAAATCGAGA 57.544 29.630 24.36 13.98 40.11 4.04
566 596 3.355378 TGATCTGCAAACCGATTTCCAT 58.645 40.909 0.00 0.00 0.00 3.41
589 619 1.271446 CTCGCTACCATGCACGATCG 61.271 60.000 14.88 14.88 33.53 3.69
590 620 1.552348 GCTCGCTACCATGCACGATC 61.552 60.000 0.00 0.00 33.53 3.69
610 640 1.652563 GGTTCGTGGTTGGACTTGC 59.347 57.895 0.00 0.00 0.00 4.01
753 787 3.749735 GAGAGAGTGAGGAGCGCGC 62.750 68.421 26.66 26.66 0.00 6.86
804 838 4.520874 GTGCTATACTGGAGTAGATGAGCA 59.479 45.833 9.63 9.63 35.49 4.26
805 839 4.520874 TGTGCTATACTGGAGTAGATGAGC 59.479 45.833 0.00 0.00 33.52 4.26
806 840 5.335583 GCTGTGCTATACTGGAGTAGATGAG 60.336 48.000 0.00 0.00 33.52 2.90
807 841 4.520874 GCTGTGCTATACTGGAGTAGATGA 59.479 45.833 0.00 0.00 33.52 2.92
808 842 4.614764 CGCTGTGCTATACTGGAGTAGATG 60.615 50.000 0.00 0.00 33.52 2.90
809 843 3.504134 CGCTGTGCTATACTGGAGTAGAT 59.496 47.826 0.00 0.00 33.52 1.98
827 861 0.873743 GCTAGCTAGCTTGGACGCTG 60.874 60.000 33.71 1.21 45.62 5.18
904 938 4.558226 TCACTGGGCCTGCTTATATATG 57.442 45.455 10.71 0.00 0.00 1.78
920 954 4.321601 GGATGGAGTAATCTCGGATCACTG 60.322 50.000 0.00 0.00 41.26 3.66
936 970 3.842007 AGATTCAGCTCAAGGATGGAG 57.158 47.619 0.00 0.00 31.38 3.86
956 990 0.863144 GAACTTGCTCGCGTTGGTTA 59.137 50.000 5.77 0.00 0.00 2.85
959 993 0.179215 GATGAACTTGCTCGCGTTGG 60.179 55.000 5.77 0.00 0.00 3.77
961 995 0.792640 CTGATGAACTTGCTCGCGTT 59.207 50.000 5.77 0.00 0.00 4.84
963 997 1.059994 GCTGATGAACTTGCTCGCG 59.940 57.895 0.00 0.00 0.00 5.87
964 998 0.801251 AAGCTGATGAACTTGCTCGC 59.199 50.000 0.00 0.00 34.38 5.03
969 1003 2.313234 CGTTGCAAGCTGATGAACTTG 58.687 47.619 0.00 0.00 44.88 3.16
970 1004 1.335324 GCGTTGCAAGCTGATGAACTT 60.335 47.619 0.00 0.00 0.00 2.66
972 1006 0.239347 AGCGTTGCAAGCTGATGAAC 59.761 50.000 18.58 0.00 44.22 3.18
1143 1182 3.003763 GAAGGTGCCCTCCTCGGT 61.004 66.667 0.00 0.00 36.74 4.69
1150 1189 1.133809 TGCTTAGGTGAAGGTGCCCT 61.134 55.000 0.00 0.00 35.49 5.19
1155 1194 1.282157 GACCCATGCTTAGGTGAAGGT 59.718 52.381 0.00 0.00 36.17 3.50
1206 1245 2.610859 ATTGGAGGGGCTGACGGT 60.611 61.111 0.00 0.00 0.00 4.83
1257 1296 1.658102 GTCGTACACGTTGTCGCCA 60.658 57.895 1.19 0.00 41.18 5.69
1518 1557 2.254546 TGTAGAACACCAGCCAGTTG 57.745 50.000 0.00 0.00 0.00 3.16
1527 1566 1.012486 CGTCGGCCTTGTAGAACACC 61.012 60.000 0.00 0.00 0.00 4.16
1587 1626 0.543749 GGAGATCCCACCACTTCTGG 59.456 60.000 0.00 0.00 44.26 3.86
1687 1726 1.200948 CTGTTAAAGGCCTGAAGCAGC 59.799 52.381 5.69 0.00 46.50 5.25
1696 1739 7.534085 GCCATTAAAAATACTGTTAAAGGCC 57.466 36.000 2.37 0.00 43.41 5.19
1736 1783 1.519455 CAGGAGATCAACGTCCGGC 60.519 63.158 0.00 0.00 37.97 6.13
1737 1784 0.458543 CACAGGAGATCAACGTCCGG 60.459 60.000 0.00 0.00 37.97 5.14
1739 1786 0.037326 TGCACAGGAGATCAACGTCC 60.037 55.000 0.00 0.00 0.00 4.79
1754 1801 0.313987 AAAAACCTAAGCGCCTGCAC 59.686 50.000 2.29 0.00 46.23 4.57
1756 1803 0.596082 TGAAAAACCTAAGCGCCTGC 59.404 50.000 2.29 0.00 43.24 4.85
1939 1986 1.626654 CGACGGTGTTGGTGATGAGC 61.627 60.000 0.00 0.00 0.00 4.26
2038 2085 3.499737 GCGAACCTGATGCCGTGG 61.500 66.667 0.00 0.00 0.00 4.94
2061 2108 2.853731 AGCTACGACGAGGAATGAAG 57.146 50.000 0.00 0.00 0.00 3.02
2088 2135 6.606395 ACCGGAGTGGAGTATATATAACATCC 59.394 42.308 9.46 10.81 42.00 3.51
2121 2168 2.401766 GCGAGCACCCAATGTCAGG 61.402 63.158 0.00 0.00 0.00 3.86
2138 2189 2.699809 CGATGCTGCAACGAGAGC 59.300 61.111 25.20 0.00 31.46 4.09
2140 2191 2.125552 CCCGATGCTGCAACGAGA 60.126 61.111 29.82 0.00 31.46 4.04
2141 2192 2.125552 TCCCGATGCTGCAACGAG 60.126 61.111 29.82 19.45 31.46 4.18
2142 2193 2.125552 CTCCCGATGCTGCAACGA 60.126 61.111 29.82 12.81 31.46 3.85
2143 2194 3.869272 GCTCCCGATGCTGCAACG 61.869 66.667 23.01 23.01 0.00 4.10
2144 2195 3.512516 GGCTCCCGATGCTGCAAC 61.513 66.667 6.36 2.36 0.00 4.17
2145 2196 3.720601 AGGCTCCCGATGCTGCAA 61.721 61.111 6.36 0.00 0.00 4.08
2146 2197 4.478371 CAGGCTCCCGATGCTGCA 62.478 66.667 4.13 4.13 0.00 4.41
2632 2683 3.124297 CAGTAACACTTCAAGCTGCTAGC 59.876 47.826 8.10 8.10 42.84 3.42
2751 2806 8.015185 AGGTAATTTATACTACACACGACCAT 57.985 34.615 0.00 0.00 0.00 3.55
2825 2880 5.459107 GCTGTATATTCTGGTAACTGTCACG 59.541 44.000 0.00 0.00 36.78 4.35
2972 3045 1.819928 TGTACTGCCATTGCGAATGT 58.180 45.000 0.00 0.00 41.78 2.71
3063 3164 1.535444 TTGGCTTCGGTGAGAGGGA 60.535 57.895 0.00 0.00 0.00 4.20
3081 3182 8.790718 TCGAGTGTCTACTACAACTAATTTTCT 58.209 33.333 0.00 0.00 40.63 2.52
3087 3188 6.462500 ACTCTCGAGTGTCTACTACAACTAA 58.538 40.000 14.16 0.00 40.63 2.24
3089 3190 4.897140 ACTCTCGAGTGTCTACTACAACT 58.103 43.478 14.16 0.00 40.63 3.16
3126 3228 0.107263 TTGCTGTTCTGGTGTGCTGA 60.107 50.000 0.00 0.00 0.00 4.26
3171 3273 3.742882 CACTCATGCCTATGAATACACGG 59.257 47.826 0.00 0.00 42.48 4.94
3172 3274 4.371786 ACACTCATGCCTATGAATACACG 58.628 43.478 0.00 0.00 42.48 4.49
3173 3275 6.931281 ACATACACTCATGCCTATGAATACAC 59.069 38.462 0.00 0.00 42.48 2.90
3177 3280 7.605309 CACATACATACACTCATGCCTATGAAT 59.395 37.037 0.00 0.00 42.48 2.57
3186 3289 5.063312 TCGCAAACACATACATACACTCATG 59.937 40.000 0.00 0.00 0.00 3.07
3290 3394 3.571590 ACTCTAGATGGAATTCCGAGCT 58.428 45.455 19.57 17.31 39.43 4.09
3325 3429 8.686334 ACTTGTTCACAGACTTCACAAAAATAT 58.314 29.630 0.00 0.00 0.00 1.28
3329 3433 5.957842 ACTTGTTCACAGACTTCACAAAA 57.042 34.783 0.00 0.00 0.00 2.44
3332 3436 4.439057 GGTACTTGTTCACAGACTTCACA 58.561 43.478 0.00 0.00 0.00 3.58
3383 3520 1.270550 CATCTTTCAGGGCCACAACAC 59.729 52.381 6.18 0.00 0.00 3.32
3385 3522 0.890683 CCATCTTTCAGGGCCACAAC 59.109 55.000 6.18 0.00 0.00 3.32
3436 3573 3.507233 CCATGGCAGTACAAAGAACACAT 59.493 43.478 0.00 0.00 0.00 3.21
3450 3587 5.995565 ATCCATTCATTATTCCATGGCAG 57.004 39.130 6.96 0.00 36.81 4.85
3494 3635 6.052360 CAGAGCTTAAAGAAGGGTCTAATCC 58.948 44.000 0.00 0.00 36.29 3.01
3580 3722 1.466167 ACATTGTTGACAGAGATGCGC 59.534 47.619 0.00 0.00 0.00 6.09
3602 3744 6.530019 TGTCATCAGCAAGTAGTCTATGAA 57.470 37.500 0.00 0.00 0.00 2.57
3603 3745 6.530019 TTGTCATCAGCAAGTAGTCTATGA 57.470 37.500 0.00 0.00 0.00 2.15
3604 3746 6.815641 AGTTTGTCATCAGCAAGTAGTCTATG 59.184 38.462 0.00 0.00 0.00 2.23
3605 3747 6.940739 AGTTTGTCATCAGCAAGTAGTCTAT 58.059 36.000 0.00 0.00 0.00 1.98
3606 3748 6.346477 AGTTTGTCATCAGCAAGTAGTCTA 57.654 37.500 0.00 0.00 0.00 2.59
3607 3749 5.220710 AGTTTGTCATCAGCAAGTAGTCT 57.779 39.130 0.00 0.00 0.00 3.24
3608 3750 5.931441 AAGTTTGTCATCAGCAAGTAGTC 57.069 39.130 0.00 0.00 0.00 2.59
3609 3751 5.590259 ACAAAGTTTGTCATCAGCAAGTAGT 59.410 36.000 15.58 0.00 40.56 2.73
3610 3752 6.064846 ACAAAGTTTGTCATCAGCAAGTAG 57.935 37.500 15.58 0.00 40.56 2.57


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

AutoCloner maintained by Alex Coulton.