Multiple sequence alignment - TraesCS5A01G332900

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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 TraesCS5A01G332900 chr5A 100.000 2423 0 0 1 2423 541939014 541941436 0.000000e+00 4475.0
1 TraesCS5A01G332900 chr5A 79.330 179 23 11 2094 2265 543715334 543715505 1.970000e-21 113.0
2 TraesCS5A01G332900 chr5B 91.468 1758 116 16 1 1749 517195985 517197717 0.000000e+00 2385.0
3 TraesCS5A01G332900 chr5B 91.265 664 38 11 1761 2420 517199195 517199842 0.000000e+00 887.0
4 TraesCS5A01G332900 chr3D 95.817 263 11 0 980 1242 571996170 571996432 2.230000e-115 425.0
5 TraesCS5A01G332900 chr3D 78.199 211 38 7 289 494 476473673 476473466 7.030000e-26 128.0
6 TraesCS5A01G332900 chr5D 95.057 263 13 0 980 1242 329259824 329260086 4.820000e-112 414.0
7 TraesCS5A01G332900 chr5D 83.080 461 59 14 1 448 427522960 427523414 3.750000e-108 401.0
8 TraesCS5A01G332900 chr5D 76.966 178 29 9 2094 2265 428308367 428308538 9.230000e-15 91.6
9 TraesCS5A01G332900 chr5D 78.906 128 22 5 2085 2210 428376056 428376180 5.550000e-12 82.4
10 TraesCS5A01G332900 chr7A 77.742 310 59 9 191 494 712306099 712306404 5.320000e-42 182.0
11 TraesCS5A01G332900 chr1B 84.058 69 11 0 213 281 645083032 645083100 1.550000e-07 67.6


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 TraesCS5A01G332900 chr5A 541939014 541941436 2422 False 4475 4475 100.0000 1 2423 1 chr5A.!!$F1 2422
1 TraesCS5A01G332900 chr5B 517195985 517199842 3857 False 1636 2385 91.3665 1 2420 2 chr5B.!!$F1 2419

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
595 596 0.107945 GCCACAACAACTTTTGCCCA 60.108 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 3718 0.320771 AAACTCTCGCATGAACGGCT 60.321 50.0 0.0 0.0 0.0 5.52 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
32 33 7.378966 ACTACATACCATGACATATGTGTAGC 58.621 38.462 22.57 0.00 41.15 3.58
33 34 5.230182 ACATACCATGACATATGTGTAGCG 58.770 41.667 14.43 7.27 39.88 4.26
34 35 5.010617 ACATACCATGACATATGTGTAGCGA 59.989 40.000 14.43 0.00 39.88 4.93
35 36 4.607293 ACCATGACATATGTGTAGCGAT 57.393 40.909 14.43 0.00 39.09 4.58
36 37 5.722021 ACCATGACATATGTGTAGCGATA 57.278 39.130 14.43 0.00 39.09 2.92
37 38 6.096673 ACCATGACATATGTGTAGCGATAA 57.903 37.500 14.43 0.00 39.09 1.75
38 39 6.701340 ACCATGACATATGTGTAGCGATAAT 58.299 36.000 14.43 0.00 39.09 1.28
39 40 7.161404 ACCATGACATATGTGTAGCGATAATT 58.839 34.615 14.43 0.00 39.09 1.40
40 41 7.118245 ACCATGACATATGTGTAGCGATAATTG 59.882 37.037 14.43 0.00 39.09 2.32
41 42 7.118245 CCATGACATATGTGTAGCGATAATTGT 59.882 37.037 14.43 0.00 39.09 2.71
42 43 7.637709 TGACATATGTGTAGCGATAATTGTC 57.362 36.000 14.43 0.00 39.09 3.18
93 94 7.295322 TCTAATGTACTGCATCAAGCTATCT 57.705 36.000 0.00 0.00 45.94 1.98
157 158 1.599797 CCAGGTGTCCGGTGTTTCC 60.600 63.158 0.00 0.00 0.00 3.13
167 168 1.562672 CGGTGTTTCCTCCTCCCCAT 61.563 60.000 0.00 0.00 0.00 4.00
172 173 1.357761 GTTTCCTCCTCCCCATGGAAA 59.642 52.381 15.22 0.00 42.26 3.13
175 176 1.002857 CCTCCTCCCCATGGAAAGTT 58.997 55.000 15.22 0.00 41.17 2.66
176 177 1.064389 CCTCCTCCCCATGGAAAGTTC 60.064 57.143 15.22 0.00 41.17 3.01
203 204 8.669946 CTAAATGATTAGGTTTTCTCCTCCTC 57.330 38.462 0.00 0.00 38.86 3.71
204 205 5.638530 ATGATTAGGTTTTCTCCTCCTCC 57.361 43.478 0.00 0.00 38.86 4.30
205 206 3.780850 TGATTAGGTTTTCTCCTCCTCCC 59.219 47.826 0.00 0.00 38.86 4.30
206 207 3.285290 TTAGGTTTTCTCCTCCTCCCA 57.715 47.619 0.00 0.00 38.86 4.37
241 242 3.833645 CCGTCCCGCCTTCGATGA 61.834 66.667 0.00 0.00 38.10 2.92
250 251 3.978199 CGCCTTCGATGACCTTTGGGT 62.978 57.143 0.00 0.00 43.21 4.51
298 299 1.218316 GTTGGCTAGAGGGACCACG 59.782 63.158 0.00 0.00 31.83 4.94
320 321 7.169982 CCACGCTCTCATTCTTATTAGGTTTAG 59.830 40.741 0.00 0.00 0.00 1.85
338 339 1.115326 AGCCTCTTTGTTGGGGTTGC 61.115 55.000 0.00 0.00 0.00 4.17
339 340 1.398958 GCCTCTTTGTTGGGGTTGCA 61.399 55.000 0.00 0.00 0.00 4.08
343 344 0.603439 CTTTGTTGGGGTTGCATGGC 60.603 55.000 0.00 0.00 0.00 4.40
376 377 9.255304 GATGTCTCTTTGTAGGAATAATGTCTC 57.745 37.037 0.00 0.00 0.00 3.36
378 379 6.987404 GTCTCTTTGTAGGAATAATGTCTCCC 59.013 42.308 0.00 0.00 31.50 4.30
380 381 6.650120 TCTTTGTAGGAATAATGTCTCCCAC 58.350 40.000 0.00 0.00 31.50 4.61
381 382 6.214615 TCTTTGTAGGAATAATGTCTCCCACA 59.785 38.462 0.00 0.00 40.18 4.17
387 388 4.080863 GGAATAATGTCTCCCACACTCAGT 60.081 45.833 0.00 0.00 38.04 3.41
404 405 1.349026 CAGTCCCTTCACTGATGGTGT 59.651 52.381 9.54 0.00 45.92 4.16
406 407 2.154462 GTCCCTTCACTGATGGTGTTG 58.846 52.381 9.54 0.00 45.50 3.33
408 409 0.883833 CCTTCACTGATGGTGTTGGC 59.116 55.000 3.23 0.00 45.50 4.52
447 448 2.478831 GAAGTGCTTCTCCATCGGATC 58.521 52.381 4.80 0.00 36.69 3.36
464 465 0.108585 ATCATCCGGGATTTGGTCGG 59.891 55.000 6.84 0.00 44.59 4.79
470 471 2.046285 GGGATTTGGTCGGTGCTGG 61.046 63.158 0.00 0.00 0.00 4.85
471 472 1.303317 GGATTTGGTCGGTGCTGGT 60.303 57.895 0.00 0.00 0.00 4.00
494 495 5.946377 GTCTTTGATGGACCTAGTTTGGATT 59.054 40.000 0.00 0.00 0.00 3.01
530 531 2.367241 TCGGTGATGGTTGTTCTTCTGA 59.633 45.455 0.00 0.00 0.00 3.27
537 538 1.537202 GGTTGTTCTTCTGATGCGCTT 59.463 47.619 9.73 0.55 0.00 4.68
543 544 0.725686 CTTCTGATGCGCTTGTCCTG 59.274 55.000 9.73 0.94 0.00 3.86
554 555 2.431057 CGCTTGTCCTGTAGGGTCTTAT 59.569 50.000 0.00 0.00 36.25 1.73
567 568 7.458397 TGTAGGGTCTTATCATGACAACTTTT 58.542 34.615 0.00 0.00 36.26 2.27
576 577 9.764870 CTTATCATGACAACTTTTGACTATGTG 57.235 33.333 0.00 0.00 0.00 3.21
578 579 4.829064 TGACAACTTTTGACTATGTGCC 57.171 40.909 0.00 0.00 0.00 5.01
587 588 3.207265 TGACTATGTGCCACAACAACT 57.793 42.857 0.00 0.00 32.81 3.16
591 592 4.681744 ACTATGTGCCACAACAACTTTTG 58.318 39.130 0.00 0.00 32.81 2.44
595 596 0.107945 GCCACAACAACTTTTGCCCA 60.108 50.000 0.00 0.00 0.00 5.36
604 605 3.084039 CAACTTTTGCCCAGCTCTGATA 58.916 45.455 0.00 0.00 0.00 2.15
613 614 1.055040 CAGCTCTGATAAGGGAGGGG 58.945 60.000 0.00 0.00 0.00 4.79
627 628 2.489073 GGGAGGGGCAATAATGGTAGTG 60.489 54.545 0.00 0.00 0.00 2.74
637 638 1.595093 AATGGTAGTGCGCCTTTGGC 61.595 55.000 4.18 0.00 46.75 4.52
769 771 2.024414 ACGCCTATTTGATTTGGAGCC 58.976 47.619 0.00 0.00 0.00 4.70
770 772 1.338020 CGCCTATTTGATTTGGAGCCC 59.662 52.381 0.00 0.00 0.00 5.19
780 782 2.588464 TTTGGAGCCCGGTTTGATAA 57.412 45.000 0.00 0.00 0.00 1.75
784 786 3.547746 TGGAGCCCGGTTTGATAATTAC 58.452 45.455 0.00 0.00 0.00 1.89
785 787 3.201266 TGGAGCCCGGTTTGATAATTACT 59.799 43.478 0.00 0.00 0.00 2.24
880 882 7.838696 TGAAAGCCCATCCTAAATAGAAAATGA 59.161 33.333 0.00 0.00 0.00 2.57
907 909 7.218204 CGAAAATTAATAAAGCCAACCTTCTCG 59.782 37.037 0.00 0.00 31.99 4.04
937 939 6.090358 CGAAGAATAAAAACGTAGCCTTCTCA 59.910 38.462 0.00 0.00 0.00 3.27
1154 1156 0.388294 CAGCTCATCCATCTCAGCGA 59.612 55.000 0.00 0.00 36.95 4.93
1283 1285 1.007849 CGGTTTTCCTTGGCGGTTG 60.008 57.895 0.00 0.00 37.95 3.77
1286 1288 3.492311 TTTTCCTTGGCGGTTGCGC 62.492 57.895 0.00 0.00 44.10 6.09
1317 1319 1.412343 GAAGATGAGGAGCAGGAGGTC 59.588 57.143 0.00 0.00 41.49 3.85
1437 1439 1.392710 ATTAGGCGACGAGGTGGAGG 61.393 60.000 0.00 0.00 0.00 4.30
1520 1522 3.282745 TTCGTGCTCGCAGTCCTCC 62.283 63.158 2.69 0.00 36.96 4.30
1624 1630 3.222603 AGTTCCATCCCTTGTTTGTGTC 58.777 45.455 0.00 0.00 0.00 3.67
1653 1659 3.877559 TGATCATGACGGCTTCTGATTT 58.122 40.909 0.00 0.00 0.00 2.17
1679 1687 2.163815 ACTGATTTGTCGTCTCCTACCG 59.836 50.000 0.00 0.00 0.00 4.02
1685 1693 1.682854 TGTCGTCTCCTACCGTGTTTT 59.317 47.619 0.00 0.00 0.00 2.43
1691 1699 2.827921 TCTCCTACCGTGTTTTCCTACC 59.172 50.000 0.00 0.00 0.00 3.18
1694 1702 2.093816 CCTACCGTGTTTTCCTACCTCC 60.094 54.545 0.00 0.00 0.00 4.30
1698 1706 2.830321 CCGTGTTTTCCTACCTCCTACT 59.170 50.000 0.00 0.00 0.00 2.57
1722 1730 2.075426 ATCGATGATCTCCGTGCGCA 62.075 55.000 5.66 5.66 0.00 6.09
1749 1757 1.369321 GATCAGATCAGGTCCGGCC 59.631 63.158 5.44 0.59 37.58 6.13
1773 3247 1.477295 GCTTCGGTTAGGTAGCTCTGT 59.523 52.381 0.00 0.00 0.00 3.41
1778 3252 1.646189 GTTAGGTAGCTCTGTGCAGC 58.354 55.000 0.00 0.00 45.94 5.25
1914 3390 1.896465 AGTAAGAGCACTGGTCTGGAC 59.104 52.381 11.50 12.13 39.62 4.02
1916 3392 1.428869 AAGAGCACTGGTCTGGACTT 58.571 50.000 11.50 0.00 39.62 3.01
1924 3400 2.040412 ACTGGTCTGGACTTCAATTCCC 59.960 50.000 0.67 0.00 31.33 3.97
1933 3409 1.153329 TTCAATTCCCGGCGCGTAT 60.153 52.632 8.43 0.00 0.00 3.06
1934 3410 1.433053 TTCAATTCCCGGCGCGTATG 61.433 55.000 8.43 0.00 0.00 2.39
1942 3418 2.890474 GGCGCGTATGTGGTCAGG 60.890 66.667 8.43 0.00 0.00 3.86
1957 3433 1.078497 CAGGGATGCTTGCGGTGTA 60.078 57.895 0.00 0.00 0.00 2.90
1971 3448 4.130857 TGCGGTGTACTTGATCAAAAGAA 58.869 39.130 9.88 0.00 0.00 2.52
1983 3460 6.331369 TGATCAAAAGAATTTGTGGAGGAC 57.669 37.500 0.00 0.00 45.02 3.85
1991 3468 0.320374 TTTGTGGAGGACCTAGCACG 59.680 55.000 0.00 0.00 37.04 5.34
2054 3531 0.172803 ACAGGCTTCTTACTACGGCG 59.827 55.000 4.80 4.80 0.00 6.46
2081 3558 4.681942 CAGCGAGGTTCCGATCTAATTAAG 59.318 45.833 0.00 0.00 0.00 1.85
2112 3589 2.752903 GCCATACTGGTTTGGTCGATTT 59.247 45.455 10.83 0.00 40.46 2.17
2124 3601 1.536284 GGTCGATTTAGGCGAGTCCAG 60.536 57.143 0.00 0.00 38.59 3.86
2131 3608 3.764237 TTAGGCGAGTCCAGTTTCTTT 57.236 42.857 0.00 0.00 37.29 2.52
2188 3665 0.842030 AGCAGAGACAATGGTGGGGA 60.842 55.000 0.00 0.00 0.00 4.81
2241 3718 1.685224 CTGGAGGTAGGCAGGCAAA 59.315 57.895 0.00 0.00 0.00 3.68
2255 3732 1.512734 GCAAAGCCGTTCATGCGAG 60.513 57.895 0.00 0.00 0.00 5.03
2256 3733 1.911293 GCAAAGCCGTTCATGCGAGA 61.911 55.000 0.00 0.00 0.00 4.04
2257 3734 0.095935 CAAAGCCGTTCATGCGAGAG 59.904 55.000 0.00 0.00 0.00 3.20
2258 3735 0.320771 AAAGCCGTTCATGCGAGAGT 60.321 50.000 0.00 0.00 0.00 3.24
2259 3736 0.320771 AAGCCGTTCATGCGAGAGTT 60.321 50.000 0.00 0.00 0.00 3.01
2260 3737 0.320771 AGCCGTTCATGCGAGAGTTT 60.321 50.000 0.00 0.00 0.00 2.66
2261 3738 0.095417 GCCGTTCATGCGAGAGTTTC 59.905 55.000 0.00 0.00 0.00 2.78
2278 3755 7.317842 AGAGTTTCATTAGATCTTGCACATG 57.682 36.000 0.00 0.00 0.00 3.21
2279 3756 6.883217 AGAGTTTCATTAGATCTTGCACATGT 59.117 34.615 0.00 0.00 0.00 3.21
2281 3758 7.978982 AGTTTCATTAGATCTTGCACATGTAC 58.021 34.615 0.00 0.00 0.00 2.90
2283 3760 5.660460 TCATTAGATCTTGCACATGTACGT 58.340 37.500 0.00 0.00 0.00 3.57
2284 3761 5.519927 TCATTAGATCTTGCACATGTACGTG 59.480 40.000 13.64 13.64 40.00 4.49
2285 3762 3.592898 AGATCTTGCACATGTACGTGA 57.407 42.857 21.82 0.00 39.34 4.35
2292 3769 2.494073 TGCACATGTACGTGATGTCCTA 59.506 45.455 21.82 0.00 39.34 2.94
2304 3781 5.522460 ACGTGATGTCCTATTAAATCCAACG 59.478 40.000 0.00 0.00 0.00 4.10
2320 3797 2.348666 CCAACGAGCTTATCTTTGACCG 59.651 50.000 0.00 0.00 39.02 4.79
2336 3813 3.606886 CCGCTAAGGTGTGACTGTT 57.393 52.632 0.00 0.00 34.51 3.16
2339 3816 2.334838 CGCTAAGGTGTGACTGTTACC 58.665 52.381 0.00 1.51 34.68 2.85
2340 3817 2.334838 GCTAAGGTGTGACTGTTACCG 58.665 52.381 0.00 0.00 39.46 4.02
2360 3837 4.586421 ACCGATCATGACTGATGACTACAT 59.414 41.667 0.00 0.00 44.12 2.29
2398 3875 8.413309 AATTCTTCAGGTTGAAATGATCTGAA 57.587 30.769 0.00 0.00 40.70 3.02
2420 3898 4.611943 ACGATGGATCATTCTCAGTTACG 58.388 43.478 0.00 0.00 0.00 3.18
2421 3899 4.098044 ACGATGGATCATTCTCAGTTACGT 59.902 41.667 0.00 0.00 0.00 3.57
2422 3900 5.298527 ACGATGGATCATTCTCAGTTACGTA 59.701 40.000 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.881777 TCTCCCTCTATCGACAATTATCG 57.118 43.478 0.00 0.00 43.63 2.92
33 34 7.222000 ACTTCTCCCTCTATCGACAATTATC 57.778 40.000 0.00 0.00 0.00 1.75
34 35 7.437748 CAACTTCTCCCTCTATCGACAATTAT 58.562 38.462 0.00 0.00 0.00 1.28
35 36 6.183360 CCAACTTCTCCCTCTATCGACAATTA 60.183 42.308 0.00 0.00 0.00 1.40
36 37 5.395768 CCAACTTCTCCCTCTATCGACAATT 60.396 44.000 0.00 0.00 0.00 2.32
37 38 4.100189 CCAACTTCTCCCTCTATCGACAAT 59.900 45.833 0.00 0.00 0.00 2.71
38 39 3.447586 CCAACTTCTCCCTCTATCGACAA 59.552 47.826 0.00 0.00 0.00 3.18
39 40 3.024547 CCAACTTCTCCCTCTATCGACA 58.975 50.000 0.00 0.00 0.00 4.35
40 41 3.288964 TCCAACTTCTCCCTCTATCGAC 58.711 50.000 0.00 0.00 0.00 4.20
41 42 3.664551 TCCAACTTCTCCCTCTATCGA 57.335 47.619 0.00 0.00 0.00 3.59
42 43 6.597832 ATTATCCAACTTCTCCCTCTATCG 57.402 41.667 0.00 0.00 0.00 2.92
49 50 9.442047 CATTAGATGTATTATCCAACTTCTCCC 57.558 37.037 0.00 0.00 33.59 4.30
55 56 9.712305 GCAGTACATTAGATGTATTATCCAACT 57.288 33.333 4.29 0.00 46.39 3.16
93 94 7.931407 CCATAGTTACCACTATAAGTTCATGCA 59.069 37.037 0.00 0.00 43.37 3.96
104 105 5.904984 TTCATGCCCATAGTTACCACTAT 57.095 39.130 0.00 0.00 45.72 2.12
157 158 1.064389 GGAACTTTCCATGGGGAGGAG 60.064 57.143 13.02 5.63 46.01 3.69
178 179 7.717436 GGAGGAGGAGAAAACCTAATCATTTAG 59.283 40.741 0.00 0.00 40.73 1.85
191 192 1.204146 CCGATGGGAGGAGGAGAAAA 58.796 55.000 0.00 0.00 34.06 2.29
194 195 2.123251 GCCGATGGGAGGAGGAGA 60.123 66.667 0.00 0.00 34.06 3.71
198 199 4.271816 CGACGCCGATGGGAGGAG 62.272 72.222 0.00 0.00 37.45 3.69
226 227 2.202892 GGTCATCGAAGGCGGGAC 60.203 66.667 0.00 0.00 39.67 4.46
250 251 1.415672 GGTCCTCCACACCTCCACAA 61.416 60.000 0.00 0.00 0.00 3.33
279 280 1.218316 GTGGTCCCTCTAGCCAACG 59.782 63.158 0.00 0.00 33.66 4.10
286 287 0.259065 ATGAGAGCGTGGTCCCTCTA 59.741 55.000 0.00 0.00 38.48 2.43
287 288 0.616111 AATGAGAGCGTGGTCCCTCT 60.616 55.000 0.00 0.00 40.93 3.69
298 299 7.428282 GGCTAAACCTAATAAGAATGAGAGC 57.572 40.000 0.00 0.00 34.51 4.09
320 321 1.367471 GCAACCCCAACAAAGAGGC 59.633 57.895 0.00 0.00 0.00 4.70
343 344 2.509336 AAAGAGACATCGCCGCCG 60.509 61.111 0.00 0.00 0.00 6.46
349 350 7.923344 AGACATTATTCCTACAAAGAGACATCG 59.077 37.037 0.00 0.00 0.00 3.84
352 353 7.364762 GGGAGACATTATTCCTACAAAGAGACA 60.365 40.741 0.00 0.00 33.85 3.41
353 354 6.987404 GGGAGACATTATTCCTACAAAGAGAC 59.013 42.308 0.00 0.00 33.85 3.36
355 356 6.763610 GTGGGAGACATTATTCCTACAAAGAG 59.236 42.308 2.63 0.00 42.58 2.85
356 357 6.650120 GTGGGAGACATTATTCCTACAAAGA 58.350 40.000 2.63 0.00 42.58 2.52
357 358 6.927294 GTGGGAGACATTATTCCTACAAAG 57.073 41.667 2.63 0.00 42.58 2.77
376 377 0.035458 GTGAAGGGACTGAGTGTGGG 59.965 60.000 0.00 0.00 40.86 4.61
378 379 1.688735 TCAGTGAAGGGACTGAGTGTG 59.311 52.381 0.00 0.00 45.96 3.82
404 405 4.373116 GCCCTCTGACGACGCCAA 62.373 66.667 0.00 0.00 0.00 4.52
406 407 4.148825 ATGCCCTCTGACGACGCC 62.149 66.667 0.00 0.00 0.00 5.68
408 409 1.807165 CACATGCCCTCTGACGACG 60.807 63.158 0.00 0.00 0.00 5.12
447 448 1.095228 CACCGACCAAATCCCGGATG 61.095 60.000 0.73 0.00 45.58 3.51
470 471 4.906618 TCCAAACTAGGTCCATCAAAGAC 58.093 43.478 0.00 0.00 0.00 3.01
471 472 5.779241 ATCCAAACTAGGTCCATCAAAGA 57.221 39.130 0.00 0.00 0.00 2.52
485 486 4.104738 TGAAGGGAGAAGTGAATCCAAACT 59.895 41.667 0.00 0.00 37.33 2.66
494 495 1.550524 CACCGATGAAGGGAGAAGTGA 59.449 52.381 0.00 0.00 35.02 3.41
530 531 1.221840 CCCTACAGGACAAGCGCAT 59.778 57.895 11.47 0.00 38.24 4.73
537 538 4.649674 GTCATGATAAGACCCTACAGGACA 59.350 45.833 0.00 0.00 40.39 4.02
543 544 7.606456 TCAAAAGTTGTCATGATAAGACCCTAC 59.394 37.037 4.98 0.00 35.15 3.18
554 555 5.048782 GGCACATAGTCAAAAGTTGTCATGA 60.049 40.000 0.00 0.00 0.00 3.07
567 568 3.207265 AGTTGTTGTGGCACATAGTCA 57.793 42.857 22.73 14.86 44.52 3.41
576 577 0.107945 TGGGCAAAAGTTGTTGTGGC 60.108 50.000 0.00 0.00 44.22 5.01
578 579 1.134729 AGCTGGGCAAAAGTTGTTGTG 60.135 47.619 0.00 0.00 0.00 3.33
587 588 2.621407 CCCTTATCAGAGCTGGGCAAAA 60.621 50.000 0.00 0.00 0.00 2.44
591 592 0.396060 CTCCCTTATCAGAGCTGGGC 59.604 60.000 0.00 0.00 37.83 5.36
595 596 0.766288 GCCCCTCCCTTATCAGAGCT 60.766 60.000 0.00 0.00 0.00 4.09
604 605 1.318934 ACCATTATTGCCCCTCCCTT 58.681 50.000 0.00 0.00 0.00 3.95
613 614 1.308998 AGGCGCACTACCATTATTGC 58.691 50.000 10.83 0.00 31.95 3.56
628 629 2.533475 CACTAGAGTGTGCCAAAGGCG 61.533 57.143 0.00 0.00 43.83 5.52
682 684 5.586877 TGGTAGTACAAAGACCATAGGAGT 58.413 41.667 2.06 0.00 38.34 3.85
717 719 6.835819 TCGGGAGATACATTCGATCTATTT 57.164 37.500 0.00 0.00 33.71 1.40
750 752 1.338020 GGGCTCCAAATCAAATAGGCG 59.662 52.381 0.00 0.00 33.83 5.52
758 760 0.111446 TCAAACCGGGCTCCAAATCA 59.889 50.000 6.32 0.00 0.00 2.57
763 765 2.818751 AATTATCAAACCGGGCTCCA 57.181 45.000 6.32 0.00 0.00 3.86
764 766 3.813724 GAGTAATTATCAAACCGGGCTCC 59.186 47.826 6.32 0.00 0.00 4.70
769 771 7.046033 AGTACCTTGAGTAATTATCAAACCGG 58.954 38.462 0.00 0.00 36.30 5.28
770 772 8.488651 AAGTACCTTGAGTAATTATCAAACCG 57.511 34.615 9.89 5.46 37.47 4.44
785 787 9.635520 CGAAAAATACTCTTAGAAGTACCTTGA 57.364 33.333 0.00 0.00 34.68 3.02
820 822 4.391405 CAAACTTTTGCCTCCTTGACTT 57.609 40.909 0.00 0.00 0.00 3.01
852 854 8.429237 TTTTCTATTTAGGATGGGCTTTCAAA 57.571 30.769 0.00 0.00 0.00 2.69
855 857 8.138074 GTCATTTTCTATTTAGGATGGGCTTTC 58.862 37.037 0.00 0.00 0.00 2.62
880 882 7.892609 AGAAGGTTGGCTTTATTAATTTTCGT 58.107 30.769 0.00 0.00 0.00 3.85
907 909 5.058856 GGCTACGTTTTTATTCTTCGCAAAC 59.941 40.000 0.00 0.00 0.00 2.93
937 939 4.679654 CGTCGGCTAATTTCTTTTGCTTTT 59.320 37.500 0.00 0.00 36.47 2.27
1258 1260 4.629523 AAGGAAAACCGCGCCCGA 62.630 61.111 0.00 0.00 36.29 5.14
1286 1288 0.103208 CTCATCTTCCTCCCGGTTCG 59.897 60.000 0.00 0.00 0.00 3.95
1288 1290 0.042731 TCCTCATCTTCCTCCCGGTT 59.957 55.000 0.00 0.00 0.00 4.44
1302 1304 3.071206 GCGACCTCCTGCTCCTCA 61.071 66.667 0.00 0.00 0.00 3.86
1406 1408 3.676324 CGTCGCCTAATCCTTTCTGTTCT 60.676 47.826 0.00 0.00 0.00 3.01
1437 1439 0.834612 TCTCGTCTCTCCTCTCCTCC 59.165 60.000 0.00 0.00 0.00 4.30
1497 1499 1.071567 GACTGCGAGCACGAACTACC 61.072 60.000 8.01 0.00 42.66 3.18
1501 1503 2.049063 AGGACTGCGAGCACGAAC 60.049 61.111 8.01 0.00 42.66 3.95
1573 1575 7.604927 ACCAATTAGTACGTCTTATTGCAAAGA 59.395 33.333 1.71 0.00 40.02 2.52
1574 1576 7.748847 ACCAATTAGTACGTCTTATTGCAAAG 58.251 34.615 1.71 0.00 40.02 2.77
1575 1577 7.675962 ACCAATTAGTACGTCTTATTGCAAA 57.324 32.000 1.71 0.00 40.02 3.68
1576 1578 7.361371 CCAACCAATTAGTACGTCTTATTGCAA 60.361 37.037 0.00 0.00 40.02 4.08
1624 1630 1.061131 GCCGTCATGATCAACAGTTCG 59.939 52.381 0.00 0.00 0.00 3.95
1653 1659 3.574396 AGGAGACGACAAATCAGTTCTGA 59.426 43.478 4.96 4.96 0.00 3.27
1679 1687 3.261137 AGCAGTAGGAGGTAGGAAAACAC 59.739 47.826 0.00 0.00 0.00 3.32
1685 1693 3.393609 TCGATAAGCAGTAGGAGGTAGGA 59.606 47.826 0.00 0.00 0.00 2.94
1691 1699 5.163663 GGAGATCATCGATAAGCAGTAGGAG 60.164 48.000 0.00 0.00 0.00 3.69
1694 1702 4.155099 ACGGAGATCATCGATAAGCAGTAG 59.845 45.833 13.35 0.00 0.00 2.57
1698 1706 2.608016 GCACGGAGATCATCGATAAGCA 60.608 50.000 13.35 0.00 0.00 3.91
1722 1730 0.950836 CTGATCTGATCCTCGTCGCT 59.049 55.000 14.71 0.00 0.00 4.93
1749 1757 1.207329 AGCTACCTAACCGAAGCCAAG 59.793 52.381 0.00 0.00 35.54 3.61
1750 1758 1.206371 GAGCTACCTAACCGAAGCCAA 59.794 52.381 0.00 0.00 35.54 4.52
1751 1759 0.822164 GAGCTACCTAACCGAAGCCA 59.178 55.000 0.00 0.00 35.54 4.75
1753 1761 1.477295 ACAGAGCTACCTAACCGAAGC 59.523 52.381 0.00 0.00 35.16 3.86
1754 1762 2.735762 GCACAGAGCTACCTAACCGAAG 60.736 54.545 0.00 0.00 41.15 3.79
1755 1763 1.203994 GCACAGAGCTACCTAACCGAA 59.796 52.381 0.00 0.00 41.15 4.30
1756 1764 0.815734 GCACAGAGCTACCTAACCGA 59.184 55.000 0.00 0.00 41.15 4.69
1757 1765 0.530744 TGCACAGAGCTACCTAACCG 59.469 55.000 0.00 0.00 45.94 4.44
1758 1766 1.740718 GCTGCACAGAGCTACCTAACC 60.741 57.143 0.81 0.00 45.94 2.85
1759 1767 1.646189 GCTGCACAGAGCTACCTAAC 58.354 55.000 0.81 0.00 45.94 2.34
1799 3273 2.352343 GCGGGCGCAATCGAAATC 60.352 61.111 18.47 0.22 41.49 2.17
1884 3360 5.047235 ACCAGTGCTCTTACTACGAATTTCT 60.047 40.000 0.00 0.00 0.00 2.52
1914 3390 1.157870 ATACGCGCCGGGAATTGAAG 61.158 55.000 8.58 0.00 0.00 3.02
1916 3392 1.885388 CATACGCGCCGGGAATTGA 60.885 57.895 8.58 0.00 0.00 2.57
1924 3400 3.254654 CTGACCACATACGCGCCG 61.255 66.667 5.73 0.00 0.00 6.46
1933 3409 1.303561 GCAAGCATCCCTGACCACA 60.304 57.895 0.00 0.00 0.00 4.17
1934 3410 2.401766 CGCAAGCATCCCTGACCAC 61.402 63.158 0.00 0.00 0.00 4.16
1942 3418 0.447801 CAAGTACACCGCAAGCATCC 59.552 55.000 0.00 0.00 0.00 3.51
1957 3433 6.550854 TCCTCCACAAATTCTTTTGATCAAGT 59.449 34.615 8.41 0.00 44.11 3.16
1971 3448 1.066143 CGTGCTAGGTCCTCCACAAAT 60.066 52.381 17.90 0.00 35.89 2.32
2023 3500 2.869503 AAGCCTGTACCGCCATTCCG 62.870 60.000 0.00 0.00 0.00 4.30
2024 3501 1.077716 AAGCCTGTACCGCCATTCC 60.078 57.895 0.00 0.00 0.00 3.01
2054 3531 2.962697 GATCGGAACCTCGCTGCCTC 62.963 65.000 0.00 0.00 0.00 4.70
2112 3589 2.631062 TGAAAGAAACTGGACTCGCCTA 59.369 45.455 0.00 0.00 37.63 3.93
2124 3601 5.531634 TCCTTCATGTTGCATGAAAGAAAC 58.468 37.500 20.47 0.00 37.55 2.78
2131 3608 3.076621 GTCACTCCTTCATGTTGCATGA 58.923 45.455 7.63 7.63 0.00 3.07
2188 3665 8.055181 TGGAAGCTTCTAGAACATTCCATTTAT 58.945 33.333 27.74 0.00 40.83 1.40
2223 3700 0.393537 CTTTGCCTGCCTACCTCCAG 60.394 60.000 0.00 0.00 0.00 3.86
2241 3718 0.320771 AAACTCTCGCATGAACGGCT 60.321 50.000 0.00 0.00 0.00 5.52
2247 3724 6.154203 AGATCTAATGAAACTCTCGCATGA 57.846 37.500 0.00 0.00 0.00 3.07
2255 3732 7.081526 ACATGTGCAAGATCTAATGAAACTC 57.918 36.000 0.00 0.00 0.00 3.01
2256 3733 7.201556 CGTACATGTGCAAGATCTAATGAAACT 60.202 37.037 14.55 0.00 0.00 2.66
2257 3734 6.901887 CGTACATGTGCAAGATCTAATGAAAC 59.098 38.462 14.55 0.00 0.00 2.78
2258 3735 6.593770 ACGTACATGTGCAAGATCTAATGAAA 59.406 34.615 14.55 0.00 0.00 2.69
2259 3736 6.035975 CACGTACATGTGCAAGATCTAATGAA 59.964 38.462 14.55 0.00 32.31 2.57
2260 3737 5.519927 CACGTACATGTGCAAGATCTAATGA 59.480 40.000 14.55 0.00 32.31 2.57
2261 3738 5.519927 TCACGTACATGTGCAAGATCTAATG 59.480 40.000 14.55 0.00 39.73 1.90
2278 3755 7.306399 CGTTGGATTTAATAGGACATCACGTAC 60.306 40.741 0.00 0.00 0.00 3.67
2279 3756 6.698329 CGTTGGATTTAATAGGACATCACGTA 59.302 38.462 0.00 0.00 0.00 3.57
2281 3758 5.751509 TCGTTGGATTTAATAGGACATCACG 59.248 40.000 0.00 0.00 0.00 4.35
2283 3760 5.758296 GCTCGTTGGATTTAATAGGACATCA 59.242 40.000 0.00 0.00 0.00 3.07
2284 3761 5.992217 AGCTCGTTGGATTTAATAGGACATC 59.008 40.000 0.00 0.00 0.00 3.06
2285 3762 5.930135 AGCTCGTTGGATTTAATAGGACAT 58.070 37.500 0.00 0.00 0.00 3.06
2292 3769 8.398665 GTCAAAGATAAGCTCGTTGGATTTAAT 58.601 33.333 0.00 0.00 41.83 1.40
2304 3781 3.804873 CCTTAGCGGTCAAAGATAAGCTC 59.195 47.826 0.00 0.00 36.56 4.09
2320 3797 2.029649 TCGGTAACAGTCACACCTTAGC 60.030 50.000 0.00 0.00 0.00 3.09
2336 3813 5.130350 TGTAGTCATCAGTCATGATCGGTA 58.870 41.667 0.00 0.00 44.58 4.02
2339 3816 9.846248 TTTATATGTAGTCATCAGTCATGATCG 57.154 33.333 0.00 0.00 44.58 3.69
2373 3850 8.302438 GTTCAGATCATTTCAACCTGAAGAATT 58.698 33.333 0.00 0.00 42.36 2.17
2398 3875 4.098044 ACGTAACTGAGAATGATCCATCGT 59.902 41.667 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.