Multiple sequence alignment - TraesCS6D01G154600

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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 TraesCS6D01G154600 chr6D 100.000 5199 0 0 1 5199 129780000 129785198 0.000000e+00 9601.0
1 TraesCS6D01G154600 chr6A 93.243 4928 213 65 337 5197 168114454 168119328 0.000000e+00 7145.0
2 TraesCS6D01G154600 chr6A 87.850 214 17 2 13 226 168114131 168114335 5.200000e-60 243.0
3 TraesCS6D01G154600 chr6A 88.764 89 7 1 250 335 168114335 168114423 7.120000e-19 106.0
4 TraesCS6D01G154600 chr6A 96.296 54 2 0 4351 4404 168118449 168118502 7.170000e-14 89.8
5 TraesCS6D01G154600 chr6B 97.011 2643 73 4 2558 5199 228241023 228243660 0.000000e+00 4438.0
6 TraesCS6D01G154600 chr6B 94.115 1937 74 19 651 2563 228239067 228240987 0.000000e+00 2909.0
7 TraesCS6D01G154600 chr6B 75.914 930 186 32 2895 3799 8787583 8786667 4.780000e-120 442.0
8 TraesCS6D01G154600 chr6B 85.981 321 17 10 20 335 228238466 228238763 8.400000e-83 318.0
9 TraesCS6D01G154600 chr6B 89.017 173 17 2 334 505 228238792 228238963 4.080000e-51 213.0
10 TraesCS6D01G154600 chr6B 75.079 317 62 16 3498 3806 671166177 671165870 1.170000e-26 132.0
11 TraesCS6D01G154600 chr5A 79.082 980 179 23 2861 3824 4957895 4956926 0.000000e+00 651.0
12 TraesCS6D01G154600 chr5A 76.935 633 130 14 3178 3802 29906563 29905939 3.850000e-91 346.0
13 TraesCS6D01G154600 chr5A 90.909 44 3 1 4157 4199 575706082 575706039 2.020000e-04 58.4
14 TraesCS6D01G154600 chr5A 90.909 44 3 1 4157 4199 576084920 576084877 2.020000e-04 58.4
15 TraesCS6D01G154600 chr5A 90.909 44 3 1 4157 4199 576272511 576272554 2.020000e-04 58.4
16 TraesCS6D01G154600 chr5B 77.959 980 190 21 2861 3824 7707664 7706695 1.610000e-164 590.0
17 TraesCS6D01G154600 chr5B 90.909 44 3 1 4157 4199 560441483 560441440 2.020000e-04 58.4
18 TraesCS6D01G154600 chr5B 89.362 47 3 2 4157 4202 561061827 561061782 2.020000e-04 58.4
19 TraesCS6D01G154600 chr7A 77.037 270 46 8 3178 3436 15525081 15524817 1.950000e-29 141.0
20 TraesCS6D01G154600 chr1B 93.651 63 4 0 501 563 499208800 499208862 1.540000e-15 95.3
21 TraesCS6D01G154600 chr1B 88.060 67 7 1 504 569 24159505 24159571 1.550000e-10 78.7
22 TraesCS6D01G154600 chrUn 90.909 66 6 0 504 569 27338330 27338395 7.170000e-14 89.8
23 TraesCS6D01G154600 chr2D 93.333 60 3 1 510 569 647488400 647488342 2.580000e-13 87.9
24 TraesCS6D01G154600 chr2D 87.500 72 5 2 504 571 574569822 574569751 4.320000e-11 80.5
25 TraesCS6D01G154600 chr3D 90.769 65 5 1 504 568 14221591 14221654 9.280000e-13 86.1
26 TraesCS6D01G154600 chr2A 87.671 73 7 2 501 572 580384431 580384502 3.340000e-12 84.2
27 TraesCS6D01G154600 chr5D 72.347 311 68 17 3493 3794 458180772 458180471 1.200000e-11 82.4
28 TraesCS6D01G154600 chr5D 90.909 44 3 1 4157 4199 458094833 458094790 2.020000e-04 58.4
29 TraesCS6D01G154600 chr5D 100.000 30 0 0 4170 4199 458180083 458180054 7.270000e-04 56.5
30 TraesCS6D01G154600 chr2B 88.571 70 2 4 504 568 619681480 619681412 4.320000e-11 80.5
31 TraesCS6D01G154600 chr2B 87.879 66 8 0 504 569 12076249 12076314 1.550000e-10 78.7


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 TraesCS6D01G154600 chr6D 129780000 129785198 5198 False 9601.00 9601 100.00000 1 5199 1 chr6D.!!$F1 5198
1 TraesCS6D01G154600 chr6A 168114131 168119328 5197 False 1895.95 7145 91.53825 13 5197 4 chr6A.!!$F1 5184
2 TraesCS6D01G154600 chr6B 228238466 228243660 5194 False 1969.50 4438 91.53100 20 5199 4 chr6B.!!$F1 5179
3 TraesCS6D01G154600 chr6B 8786667 8787583 916 True 442.00 442 75.91400 2895 3799 1 chr6B.!!$R1 904
4 TraesCS6D01G154600 chr5A 4956926 4957895 969 True 651.00 651 79.08200 2861 3824 1 chr5A.!!$R1 963
5 TraesCS6D01G154600 chr5A 29905939 29906563 624 True 346.00 346 76.93500 3178 3802 1 chr5A.!!$R2 624
6 TraesCS6D01G154600 chr5B 7706695 7707664 969 True 590.00 590 77.95900 2861 3824 1 chr5B.!!$R1 963

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
752 837 0.249073 AGATAGCCAAGTACGCAGCG 60.249 55.0 14.82 14.82 0.00 5.18 F
1363 1450 0.178921 TGACCCCAGTGAGCTTCTCT 60.179 55.0 0.00 0.00 0.00 3.10 F
2167 2288 0.329931 ATGGATTGCCGGTGGTTGTA 59.670 50.0 1.90 0.00 36.79 2.41 F
3829 4022 0.326927 GGAAGAACATCCCGGTGGAA 59.673 55.0 0.00 0.00 45.98 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2271 0.322187 AGTACAACCACCGGCAATCC 60.322 55.000 0.00 0.0 0.00 3.01 R
2741 2910 0.742281 ACCATGCATGCACTCTCGTC 60.742 55.000 25.37 0.0 0.00 4.20 R
3967 4160 0.030369 CCGCGTACTCTCCCATGTAC 59.970 60.000 4.92 0.0 36.59 2.90 R
5111 5342 1.342174 TCCACCGGTAACTCACTTGAC 59.658 52.381 6.87 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
150 153 2.435059 GTTGCCCTCCTGCTCGTC 60.435 66.667 0.00 0.00 0.00 4.20
181 184 0.322546 ATGTGGTTTTCTCGAGCCCC 60.323 55.000 7.81 5.11 0.00 5.80
208 211 3.128349 GTCGACTTGCCAACTTTCTACA 58.872 45.455 8.70 0.00 0.00 2.74
209 212 3.059800 GTCGACTTGCCAACTTTCTACAC 60.060 47.826 8.70 0.00 0.00 2.90
211 214 3.477530 GACTTGCCAACTTTCTACACCT 58.522 45.455 0.00 0.00 0.00 4.00
220 223 7.139392 GCCAACTTTCTACACCTTAAGAAAAG 58.861 38.462 3.36 6.49 40.27 2.27
225 228 8.622157 ACTTTCTACACCTTAAGAAAAGCTTTC 58.378 33.333 13.10 6.36 40.27 2.62
226 229 8.747538 TTTCTACACCTTAAGAAAAGCTTTCT 57.252 30.769 13.10 8.61 38.45 2.52
227 230 9.841295 TTTCTACACCTTAAGAAAAGCTTTCTA 57.159 29.630 13.10 1.96 38.45 2.10
228 231 8.828688 TCTACACCTTAAGAAAAGCTTTCTAC 57.171 34.615 13.10 7.45 38.05 2.59
229 232 8.648693 TCTACACCTTAAGAAAAGCTTTCTACT 58.351 33.333 13.10 9.61 38.05 2.57
230 233 7.497925 ACACCTTAAGAAAAGCTTTCTACTG 57.502 36.000 13.10 2.01 38.05 2.74
231 234 6.017026 ACACCTTAAGAAAAGCTTTCTACTGC 60.017 38.462 13.10 0.00 38.05 4.40
232 235 5.179555 ACCTTAAGAAAAGCTTTCTACTGCG 59.820 40.000 13.10 1.44 38.05 5.18
233 236 3.544356 AAGAAAAGCTTTCTACTGCGC 57.456 42.857 13.10 0.00 31.11 6.09
234 237 1.461127 AGAAAAGCTTTCTACTGCGCG 59.539 47.619 13.10 0.00 0.00 6.86
268 271 2.095969 CACCAGCGACGCTTATTTTGAA 60.096 45.455 21.97 0.00 36.40 2.69
320 326 3.503748 AGCTGCCTACACAAAGATCAAAC 59.496 43.478 0.00 0.00 0.00 2.93
323 329 3.496884 TGCCTACACAAAGATCAAACGTC 59.503 43.478 0.00 0.00 0.00 4.34
328 334 2.154198 CACAAAGATCAAACGTCGCGTA 59.846 45.455 5.77 0.00 39.99 4.42
348 384 1.153349 GCTCACCCGGTCTCAATCC 60.153 63.158 0.00 0.00 0.00 3.01
408 444 5.376854 AAGGACATGCAAACAATGAGTAC 57.623 39.130 0.00 0.00 0.00 2.73
411 447 4.023279 GGACATGCAAACAATGAGTACACA 60.023 41.667 0.00 0.00 0.00 3.72
429 465 7.224297 AGTACACAACACTGGAAAGTATTCAT 58.776 34.615 0.00 0.00 37.29 2.57
433 469 8.103305 ACACAACACTGGAAAGTATTCATATCT 58.897 33.333 0.00 0.00 37.29 1.98
505 542 9.819267 ACAACCAAATCTAGATTAGCTTACTAC 57.181 33.333 18.23 0.00 0.00 2.73
508 545 8.862085 ACCAAATCTAGATTAGCTTACTACTCC 58.138 37.037 18.23 0.00 30.31 3.85
509 546 8.308207 CCAAATCTAGATTAGCTTACTACTCCC 58.692 40.741 18.23 0.00 30.31 4.30
510 547 9.084533 CAAATCTAGATTAGCTTACTACTCCCT 57.915 37.037 18.23 0.00 30.31 4.20
513 550 9.914834 ATCTAGATTAGCTTACTACTCCCTATG 57.085 37.037 0.00 0.00 30.31 2.23
514 551 8.892530 TCTAGATTAGCTTACTACTCCCTATGT 58.107 37.037 0.00 0.00 30.31 2.29
517 554 9.878737 AGATTAGCTTACTACTCCCTATGTAAA 57.121 33.333 0.00 0.00 30.31 2.01
518 555 9.911138 GATTAGCTTACTACTCCCTATGTAAAC 57.089 37.037 0.00 0.00 0.00 2.01
519 556 9.657728 ATTAGCTTACTACTCCCTATGTAAACT 57.342 33.333 0.00 0.00 0.00 2.66
522 559 9.657728 AGCTTACTACTCCCTATGTAAACTAAT 57.342 33.333 0.00 0.00 0.00 1.73
560 597 8.332996 AGATCGCTCTTATATTAGTTTACGGA 57.667 34.615 0.00 0.00 0.00 4.69
561 598 8.452534 AGATCGCTCTTATATTAGTTTACGGAG 58.547 37.037 0.00 0.00 0.00 4.63
562 599 6.906659 TCGCTCTTATATTAGTTTACGGAGG 58.093 40.000 0.00 0.00 0.00 4.30
563 600 6.712095 TCGCTCTTATATTAGTTTACGGAGGA 59.288 38.462 0.00 0.00 0.00 3.71
564 601 7.229306 TCGCTCTTATATTAGTTTACGGAGGAA 59.771 37.037 0.00 0.00 0.00 3.36
565 602 7.537991 CGCTCTTATATTAGTTTACGGAGGAAG 59.462 40.741 0.00 0.00 0.00 3.46
566 603 8.358895 GCTCTTATATTAGTTTACGGAGGAAGT 58.641 37.037 0.00 0.00 0.00 3.01
615 693 6.925165 TGATTCAATTCTTTCCAGCACTTTTC 59.075 34.615 0.00 0.00 0.00 2.29
616 694 6.469782 TTCAATTCTTTCCAGCACTTTTCT 57.530 33.333 0.00 0.00 0.00 2.52
617 695 6.469782 TCAATTCTTTCCAGCACTTTTCTT 57.530 33.333 0.00 0.00 0.00 2.52
622 700 5.410067 TCTTTCCAGCACTTTTCTTTTGTG 58.590 37.500 0.00 0.00 35.08 3.33
632 710 6.693113 GCACTTTTCTTTTGTGAACTTCTAGG 59.307 38.462 0.00 0.00 33.95 3.02
643 721 0.320771 ACTTCTAGGCAAGTGCACCG 60.321 55.000 14.63 6.34 44.36 4.94
644 722 0.320771 CTTCTAGGCAAGTGCACCGT 60.321 55.000 14.63 2.45 44.36 4.83
685 763 1.138069 CCATAGGGCGTCATGTACACA 59.862 52.381 0.00 0.00 0.00 3.72
686 764 2.224281 CCATAGGGCGTCATGTACACAT 60.224 50.000 0.00 0.00 36.96 3.21
700 785 8.721478 GTCATGTACACATACACTCTTCAAATT 58.279 33.333 0.00 0.00 44.11 1.82
709 794 9.520204 ACATACACTCTTCAAATTGACTTTTTG 57.480 29.630 0.00 0.00 35.79 2.44
713 798 9.271828 ACACTCTTCAAATTGACTTTTTGTTTT 57.728 25.926 0.00 0.00 35.90 2.43
714 799 9.532697 CACTCTTCAAATTGACTTTTTGTTTTG 57.467 29.630 0.00 0.00 35.90 2.44
742 827 9.034800 AGAAAAATGATTTGGTTAGATAGCCAA 57.965 29.630 4.25 4.25 43.47 4.52
752 837 0.249073 AGATAGCCAAGTACGCAGCG 60.249 55.000 14.82 14.82 0.00 5.18
801 886 0.941936 TGACACACATACGCACGTGG 60.942 55.000 18.88 10.05 37.45 4.94
859 944 4.948341 AACTGACACACATACTACCACA 57.052 40.909 0.00 0.00 0.00 4.17
879 964 2.345244 CGCAGAGCACTTGGGAGT 59.655 61.111 0.00 0.00 36.25 3.85
910 997 2.601966 CCGGCCCTCCTAGCTAGG 60.602 72.222 30.94 30.94 45.02 3.02
1314 1401 0.832135 AGGACCTCTTCGGCAAGACA 60.832 55.000 0.00 0.00 34.71 3.41
1358 1445 1.835927 GAGCTTGACCCCAGTGAGCT 61.836 60.000 1.65 1.65 42.05 4.09
1363 1450 0.178921 TGACCCCAGTGAGCTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
1398 1492 2.108514 AACGATGGCATGCAGGACG 61.109 57.895 21.36 19.67 0.00 4.79
1472 1571 4.046462 CACATGGCTGAGAAAAGTTGTTG 58.954 43.478 0.00 0.00 0.00 3.33
1508 1607 2.270858 GGAAGGGAGAGGGAGAAAGTT 58.729 52.381 0.00 0.00 0.00 2.66
1638 1737 2.169352 AGGGAGATGTTCATCAAGGACG 59.831 50.000 14.05 0.00 0.00 4.79
2106 2222 3.987187 GGTACGTACGCACATCGG 58.013 61.111 19.66 0.00 43.86 4.18
2110 2226 2.601628 TACGTACGCACATCGGCCTG 62.602 60.000 16.72 0.00 43.86 4.85
2116 2232 2.586079 CACATCGGCCTGGCTACG 60.586 66.667 19.68 14.68 0.00 3.51
2118 2234 2.186903 CATCGGCCTGGCTACGTT 59.813 61.111 19.68 6.86 0.00 3.99
2121 2237 4.760047 CGGCCTGGCTACGTTGCT 62.760 66.667 20.87 0.00 0.00 3.91
2128 2249 1.594862 CTGGCTACGTTGCTAGCAATC 59.405 52.381 31.46 22.41 40.96 2.67
2129 2250 1.207089 TGGCTACGTTGCTAGCAATCT 59.793 47.619 31.46 21.09 40.96 2.40
2130 2251 2.429250 TGGCTACGTTGCTAGCAATCTA 59.571 45.455 31.46 21.08 40.96 1.98
2131 2252 3.053455 GGCTACGTTGCTAGCAATCTAG 58.947 50.000 31.46 28.01 44.03 2.43
2132 2253 3.053455 GCTACGTTGCTAGCAATCTAGG 58.947 50.000 31.46 17.79 42.00 3.02
2134 2255 4.261489 GCTACGTTGCTAGCAATCTAGGTA 60.261 45.833 31.46 22.07 42.00 3.08
2135 2256 4.730949 ACGTTGCTAGCAATCTAGGTAA 57.269 40.909 31.46 4.52 42.00 2.85
2136 2257 5.277857 ACGTTGCTAGCAATCTAGGTAAT 57.722 39.130 31.46 8.16 42.00 1.89
2139 2260 6.598064 ACGTTGCTAGCAATCTAGGTAATTTT 59.402 34.615 31.46 5.24 42.00 1.82
2167 2288 0.329931 ATGGATTGCCGGTGGTTGTA 59.670 50.000 1.90 0.00 36.79 2.41
2173 2294 4.504340 GGATTGCCGGTGGTTGTACTATAT 60.504 45.833 1.90 0.00 0.00 0.86
2174 2295 5.279607 GGATTGCCGGTGGTTGTACTATATA 60.280 44.000 1.90 0.00 0.00 0.86
2175 2296 5.811796 TTGCCGGTGGTTGTACTATATAT 57.188 39.130 1.90 0.00 0.00 0.86
2176 2297 6.914654 TTGCCGGTGGTTGTACTATATATA 57.085 37.500 1.90 0.00 0.00 0.86
2177 2298 7.484993 TTGCCGGTGGTTGTACTATATATAT 57.515 36.000 1.90 0.00 0.00 0.86
2178 2299 8.592529 TTGCCGGTGGTTGTACTATATATATA 57.407 34.615 1.90 2.49 0.00 0.86
2181 2302 9.075678 GCCGGTGGTTGTACTATATATATAGAT 57.924 37.037 28.76 17.97 38.30 1.98
2712 2881 3.554934 TCACAGCCTTTGATCAAGTTGT 58.445 40.909 8.41 9.48 31.72 3.32
3585 3778 2.746362 ACTTCTACTACAAGTCGGACGG 59.254 50.000 1.89 1.97 27.00 4.79
3586 3779 1.089920 TCTACTACAAGTCGGACGGC 58.910 55.000 1.89 0.00 0.00 5.68
3829 4022 0.326927 GGAAGAACATCCCGGTGGAA 59.673 55.000 0.00 0.00 45.98 3.53
3832 4025 1.358152 AGAACATCCCGGTGGAAGAA 58.642 50.000 0.00 0.00 45.98 2.52
3834 4027 2.107552 AGAACATCCCGGTGGAAGAAAA 59.892 45.455 0.00 0.00 45.98 2.29
3985 4178 1.002684 GAGTACATGGGAGAGTACGCG 60.003 57.143 3.53 3.53 43.98 6.01
4045 4238 1.328279 TCGAGAAGTTCAGTGGCAGA 58.672 50.000 5.50 0.00 0.00 4.26
4199 4392 2.356432 CCCAACAGCATCTCCATCTGAA 60.356 50.000 0.00 0.00 0.00 3.02
4217 4410 1.215423 GAATGTGGCCCCAGGATAAGT 59.785 52.381 0.00 0.00 0.00 2.24
4304 4501 4.720902 CGTGCATGACAGGGGCCA 62.721 66.667 4.39 0.00 0.00 5.36
4353 4550 4.666655 CGCTATTGTATGCCGTGAATTAGC 60.667 45.833 0.00 0.00 0.00 3.09
4403 4631 5.839063 TGACCTCATCGAATCCTAATTAGGT 59.161 40.000 27.14 12.32 44.02 3.08
4632 4861 3.827302 AGGGGCATATAGACAGAACTACG 59.173 47.826 0.00 0.00 0.00 3.51
4746 4975 3.129287 CCAACCAAGCAATACATGAGACC 59.871 47.826 0.00 0.00 0.00 3.85
4802 5031 2.614057 ACTTTTCAACCAGAGTGAAGCG 59.386 45.455 0.00 0.00 0.00 4.68
4834 5063 4.070009 AGTTTACTTTGCTTACTTCCCCG 58.930 43.478 0.00 0.00 0.00 5.73
4837 5068 3.775261 ACTTTGCTTACTTCCCCGTAA 57.225 42.857 0.00 0.00 0.00 3.18
4865 5096 2.964740 TCACATAGTGTCTTCTGCAGC 58.035 47.619 9.47 0.00 34.79 5.25
5077 5308 7.066766 ACTGATCAGAGCAATCAAATTAAGACC 59.933 37.037 29.27 0.00 32.96 3.85
5088 5319 9.695526 CAATCAAATTAAGACCAAGATGTGAAA 57.304 29.630 0.00 0.00 0.00 2.69
5111 5342 6.734104 AAGTATAAGAAAGAAGCTGCACTG 57.266 37.500 1.02 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.705664 ATACATCAGTAGGCTAGGAGACTA 57.294 41.667 0.00 0.00 33.88 2.59
11 12 5.592587 ATACATCAGTAGGCTAGGAGACT 57.407 43.478 0.00 0.00 37.37 3.24
99 100 2.184167 CACGTTCCACCACACCCAC 61.184 63.158 0.00 0.00 0.00 4.61
100 101 2.190843 CACGTTCCACCACACCCA 59.809 61.111 0.00 0.00 0.00 4.51
150 153 7.436673 TCGAGAAAACCACATAAAATTTGTTGG 59.563 33.333 0.00 0.00 0.00 3.77
194 197 5.298989 TCTTAAGGTGTAGAAAGTTGGCA 57.701 39.130 1.85 0.00 0.00 4.92
208 211 5.179555 CGCAGTAGAAAGCTTTTCTTAAGGT 59.820 40.000 14.05 0.00 33.88 3.50
209 212 5.622378 CGCAGTAGAAAGCTTTTCTTAAGG 58.378 41.667 14.05 1.93 33.88 2.69
211 214 4.377022 CGCGCAGTAGAAAGCTTTTCTTAA 60.377 41.667 14.05 0.00 33.88 1.85
220 223 2.096594 GCACGCGCAGTAGAAAGC 59.903 61.111 5.73 2.15 38.36 3.51
231 234 4.703799 TGCCAATTGCTGCACGCG 62.704 61.111 3.53 3.53 43.27 6.01
243 246 2.796483 ATAAGCGTCGCTGGTGCCAA 62.796 55.000 22.50 1.05 39.62 4.52
268 271 9.018582 GCAGCTTAAAGAATATATCCCTTCATT 57.981 33.333 0.00 0.00 0.00 2.57
328 334 2.227089 GATTGAGACCGGGTGAGCGT 62.227 60.000 3.30 0.00 0.00 5.07
335 341 3.324846 TGAATATGAGGATTGAGACCGGG 59.675 47.826 6.32 0.00 0.00 5.73
390 426 5.163571 TGTTGTGTACTCATTGTTTGCATGT 60.164 36.000 0.00 0.00 0.00 3.21
408 444 8.498054 AGATATGAATACTTTCCAGTGTTGTG 57.502 34.615 0.00 0.00 34.66 3.33
534 571 9.440773 TCCGTAAACTAATATAAGAGCGATCTA 57.559 33.333 2.34 0.00 0.00 1.98
535 572 8.332996 TCCGTAAACTAATATAAGAGCGATCT 57.667 34.615 0.00 0.00 0.00 2.75
536 573 7.697291 CCTCCGTAAACTAATATAAGAGCGATC 59.303 40.741 0.00 0.00 0.00 3.69
537 574 7.392673 TCCTCCGTAAACTAATATAAGAGCGAT 59.607 37.037 0.00 0.00 0.00 4.58
538 575 6.712095 TCCTCCGTAAACTAATATAAGAGCGA 59.288 38.462 0.00 0.00 0.00 4.93
539 576 6.906659 TCCTCCGTAAACTAATATAAGAGCG 58.093 40.000 0.00 0.00 0.00 5.03
540 577 8.358895 ACTTCCTCCGTAAACTAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
547 584 9.807649 GTTGAATACTTCCTCCGTAAACTAATA 57.192 33.333 0.00 0.00 0.00 0.98
548 585 8.316214 TGTTGAATACTTCCTCCGTAAACTAAT 58.684 33.333 0.00 0.00 0.00 1.73
549 586 7.599998 GTGTTGAATACTTCCTCCGTAAACTAA 59.400 37.037 0.00 0.00 0.00 2.24
550 587 7.092716 GTGTTGAATACTTCCTCCGTAAACTA 58.907 38.462 0.00 0.00 0.00 2.24
551 588 5.930569 GTGTTGAATACTTCCTCCGTAAACT 59.069 40.000 0.00 0.00 0.00 2.66
552 589 5.164022 CGTGTTGAATACTTCCTCCGTAAAC 60.164 44.000 0.00 0.00 0.00 2.01
553 590 4.925054 CGTGTTGAATACTTCCTCCGTAAA 59.075 41.667 0.00 0.00 0.00 2.01
554 591 4.022068 ACGTGTTGAATACTTCCTCCGTAA 60.022 41.667 0.00 0.00 0.00 3.18
555 592 3.507233 ACGTGTTGAATACTTCCTCCGTA 59.493 43.478 0.00 0.00 0.00 4.02
556 593 2.298163 ACGTGTTGAATACTTCCTCCGT 59.702 45.455 0.00 0.00 0.00 4.69
557 594 2.666508 CACGTGTTGAATACTTCCTCCG 59.333 50.000 7.58 0.00 0.00 4.63
558 595 3.921677 TCACGTGTTGAATACTTCCTCC 58.078 45.455 16.51 0.00 0.00 4.30
559 596 6.481954 AAATCACGTGTTGAATACTTCCTC 57.518 37.500 16.51 0.00 37.92 3.71
560 597 6.877611 AAAATCACGTGTTGAATACTTCCT 57.122 33.333 16.51 0.00 37.92 3.36
587 665 5.537674 AGTGCTGGAAAGAATTGAATCACTT 59.462 36.000 0.00 0.00 0.00 3.16
615 693 5.514279 CACTTGCCTAGAAGTTCACAAAAG 58.486 41.667 5.50 4.99 33.75 2.27
616 694 4.202010 GCACTTGCCTAGAAGTTCACAAAA 60.202 41.667 5.50 0.00 33.75 2.44
617 695 3.315191 GCACTTGCCTAGAAGTTCACAAA 59.685 43.478 5.50 0.00 33.75 2.83
622 700 1.807142 GGTGCACTTGCCTAGAAGTTC 59.193 52.381 17.98 0.00 41.18 3.01
632 710 3.660111 GGACCACGGTGCACTTGC 61.660 66.667 17.98 0.00 42.50 4.01
686 764 9.921637 AAACAAAAAGTCAATTTGAAGAGTGTA 57.078 25.926 0.00 0.00 39.56 2.90
714 799 9.521503 GGCTATCTAACCAAATCATTTTTCTTC 57.478 33.333 0.00 0.00 0.00 2.87
742 827 2.873367 CGATGATTCGCTGCGTACT 58.127 52.632 22.48 7.68 38.75 2.73
801 886 1.132640 GCTTCACGGCGATGTGTTC 59.867 57.895 16.62 0.00 40.74 3.18
859 944 2.164865 CTCCCAAGTGCTCTGCGTCT 62.165 60.000 0.00 0.00 0.00 4.18
879 964 2.438614 CCGGCCTCTCTCTCGTCA 60.439 66.667 0.00 0.00 0.00 4.35
926 1013 5.539193 TCGACCTCTACCTTCTTTTCTTCTT 59.461 40.000 0.00 0.00 0.00 2.52
928 1015 5.388408 TCGACCTCTACCTTCTTTTCTTC 57.612 43.478 0.00 0.00 0.00 2.87
934 1021 2.826725 CTGGTTCGACCTCTACCTTCTT 59.173 50.000 4.92 0.00 39.58 2.52
1278 1365 3.758088 CTGGATGTCGTCGAGGCCG 62.758 68.421 0.00 0.00 37.07 6.13
1358 1445 6.527023 CGTTGTAGCGAGAAAAGATAAGAGAA 59.473 38.462 0.00 0.00 0.00 2.87
1363 1450 5.518847 CCATCGTTGTAGCGAGAAAAGATAA 59.481 40.000 0.00 0.00 44.43 1.75
1398 1492 2.125753 CGCACAGTGCTCTCTCCC 60.126 66.667 23.15 0.00 42.25 4.30
1508 1607 1.743623 CATGTGCGCGAACCCCTTA 60.744 57.895 16.25 0.00 0.00 2.69
1638 1737 2.456119 CGCCGGTGATGAGCTTGAC 61.456 63.158 10.20 0.00 0.00 3.18
1995 2106 2.900716 TGTGGTCGATGTTCTTGTCA 57.099 45.000 0.00 0.00 0.00 3.58
2103 2219 4.752879 GCAACGTAGCCAGGCCGA 62.753 66.667 16.13 0.00 0.00 5.54
2106 2222 2.174319 GCTAGCAACGTAGCCAGGC 61.174 63.158 10.63 1.84 39.74 4.85
2110 2226 1.941325 AGATTGCTAGCAACGTAGCC 58.059 50.000 31.51 15.73 44.23 3.93
2134 2255 9.237187 ACCGGCAATCCATTAAATTTTAAAATT 57.763 25.926 18.40 18.40 40.15 1.82
2135 2256 8.672815 CACCGGCAATCCATTAAATTTTAAAAT 58.327 29.630 7.64 7.64 0.00 1.82
2136 2257 7.119846 CCACCGGCAATCCATTAAATTTTAAAA 59.880 33.333 0.00 2.51 0.00 1.52
2139 2260 5.187967 ACCACCGGCAATCCATTAAATTTTA 59.812 36.000 0.00 0.00 0.00 1.52
2146 2267 1.272203 ACAACCACCGGCAATCCATTA 60.272 47.619 0.00 0.00 0.00 1.90
2147 2268 0.541764 ACAACCACCGGCAATCCATT 60.542 50.000 0.00 0.00 0.00 3.16
2149 2270 0.606944 GTACAACCACCGGCAATCCA 60.607 55.000 0.00 0.00 0.00 3.41
2150 2271 0.322187 AGTACAACCACCGGCAATCC 60.322 55.000 0.00 0.00 0.00 3.01
2533 2654 1.651240 TACTACGTGCTCTGGCGGAC 61.651 60.000 0.00 0.00 42.25 4.79
2548 2669 6.505044 AAGTCATGTCACGTATGTGTACTA 57.495 37.500 14.63 1.18 46.49 1.82
2730 2899 4.491676 TGCACTCTCGTCAATTAACTACC 58.508 43.478 0.00 0.00 0.00 3.18
2733 2902 3.372206 GCATGCACTCTCGTCAATTAACT 59.628 43.478 14.21 0.00 0.00 2.24
2734 2903 3.125146 TGCATGCACTCTCGTCAATTAAC 59.875 43.478 18.46 0.00 0.00 2.01
2735 2904 3.333804 TGCATGCACTCTCGTCAATTAA 58.666 40.909 18.46 0.00 0.00 1.40
2741 2910 0.742281 ACCATGCATGCACTCTCGTC 60.742 55.000 25.37 0.00 0.00 4.20
3397 3590 3.414700 GTGTCGAACTGCCAGGCG 61.415 66.667 7.03 4.22 0.00 5.52
3813 4006 1.358152 TTCTTCCACCGGGATGTTCT 58.642 50.000 6.32 0.00 44.48 3.01
3829 4022 1.263356 TCTCATCGTCCCGGTTTTCT 58.737 50.000 0.00 0.00 0.00 2.52
3832 4025 1.191535 TCATCTCATCGTCCCGGTTT 58.808 50.000 0.00 0.00 0.00 3.27
3834 4027 0.747255 CTTCATCTCATCGTCCCGGT 59.253 55.000 0.00 0.00 0.00 5.28
3844 4037 4.290711 TGCCATGAACTTCTTCATCTCA 57.709 40.909 0.00 0.00 44.04 3.27
3967 4160 0.030369 CCGCGTACTCTCCCATGTAC 59.970 60.000 4.92 0.00 36.59 2.90
4045 4238 1.920835 GCCCTCCACCTCCTTCAGT 60.921 63.158 0.00 0.00 0.00 3.41
4048 4241 2.671682 GTGCCCTCCACCTCCTTC 59.328 66.667 0.00 0.00 38.55 3.46
4199 4392 1.308877 AACTTATCCTGGGGCCACAT 58.691 50.000 8.98 0.00 0.00 3.21
4304 4501 3.053245 ACACACTAGTAGATGCCTCTCCT 60.053 47.826 3.59 0.00 32.66 3.69
4403 4631 5.755409 TGTAGATGCCCACTCTTTCTTAA 57.245 39.130 0.00 0.00 0.00 1.85
4632 4861 5.287226 CACGTATACCCATTCTCCACTTAC 58.713 45.833 0.00 0.00 0.00 2.34
4746 4975 6.724263 TGGCAATCAGTATTATTAGCGTTTG 58.276 36.000 0.00 0.00 0.00 2.93
4802 5031 2.437413 CAAAGTAAACTCTGCTCCCCC 58.563 52.381 0.00 0.00 0.00 5.40
4834 5063 5.524284 AGACACTATGTGATGCTCGATTAC 58.476 41.667 4.61 0.00 36.96 1.89
4837 5068 4.340666 AGAAGACACTATGTGATGCTCGAT 59.659 41.667 4.61 0.00 36.96 3.59
4887 5118 1.666888 GCCAATTGACGACAGCCAAAG 60.667 52.381 7.12 0.00 0.00 2.77
5088 5319 6.234177 ACAGTGCAGCTTCTTTCTTATACTT 58.766 36.000 0.00 0.00 0.00 2.24
5111 5342 1.342174 TCCACCGGTAACTCACTTGAC 59.658 52.381 6.87 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.