Multiple sequence alignment - TraesCS2D01G600900

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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 TraesCS2D01G600900 chr2D 100.000 4007 0 0 1 4007 651416290 651420296 0.000000e+00 7400.0
1 TraesCS2D01G600900 chr2D 93.395 651 15 13 3141 3768 461295032 461294387 0.000000e+00 939.0
2 TraesCS2D01G600900 chr2A 92.361 3194 166 31 1 3139 776219505 776216335 0.000000e+00 4475.0
3 TraesCS2D01G600900 chr2A 91.433 607 40 6 2405 3010 776550473 776551068 0.000000e+00 822.0
4 TraesCS2D01G600900 chr2A 88.489 556 37 3 1830 2385 776549081 776549609 0.000000e+00 647.0
5 TraesCS2D01G600900 chr2B 95.233 1930 77 8 1097 3017 780667762 780665839 0.000000e+00 3040.0
6 TraesCS2D01G600900 chr2B 90.328 1923 143 16 1217 3139 780975567 780977446 0.000000e+00 2481.0
7 TraesCS2D01G600900 chr2B 85.025 788 86 26 3143 3914 794338685 794339456 0.000000e+00 773.0
8 TraesCS2D01G600900 chr2B 88.283 367 20 12 1 352 780822280 780822638 6.190000e-113 418.0
9 TraesCS2D01G600900 chr2B 87.379 103 10 3 3905 4007 794339477 794339576 9.100000e-22 115.0
10 TraesCS2D01G600900 chr1D 90.218 2249 102 29 777 3013 493954054 493951912 0.000000e+00 2826.0
11 TraesCS2D01G600900 chr7A 82.978 1827 283 19 1116 2925 624967000 624965185 0.000000e+00 1626.0
12 TraesCS2D01G600900 chr7B 82.749 1826 285 21 1118 2925 586659733 586661546 0.000000e+00 1600.0
13 TraesCS2D01G600900 chr7B 82.549 1828 289 21 1116 2925 586265673 586263858 0.000000e+00 1581.0
14 TraesCS2D01G600900 chr7B 83.885 906 88 34 3143 4007 385621822 385622710 0.000000e+00 811.0
15 TraesCS2D01G600900 chr7B 83.295 874 83 31 3143 3973 10057025 10057878 0.000000e+00 747.0
16 TraesCS2D01G600900 chr7D 82.279 1834 291 24 1111 2925 543602370 543604188 0.000000e+00 1555.0
17 TraesCS2D01G600900 chr7D 82.276 1828 294 21 1116 2925 543059521 543057706 0.000000e+00 1554.0
18 TraesCS2D01G600900 chr5A 82.112 1828 297 21 1116 2925 505627933 505626118 0.000000e+00 1537.0
19 TraesCS2D01G600900 chr1B 94.822 927 30 4 1011 1937 559585617 559586525 0.000000e+00 1430.0
20 TraesCS2D01G600900 chr1B 83.696 920 77 39 3143 4007 190313968 190314869 0.000000e+00 800.0
21 TraesCS2D01G600900 chr1B 83.150 908 88 38 3143 4007 484265836 484264951 0.000000e+00 769.0
22 TraesCS2D01G600900 chr1B 92.000 150 10 2 3 151 559579184 559579332 4.060000e-50 209.0
23 TraesCS2D01G600900 chr1B 98.058 103 2 0 180 282 559579328 559579430 3.180000e-41 180.0
24 TraesCS2D01G600900 chr6B 81.761 477 58 20 3308 3768 29279321 29279784 4.890000e-99 372.0
25 TraesCS2D01G600900 chr5D 100.000 37 0 0 3106 3142 297937640 297937604 7.190000e-08 69.4


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 TraesCS2D01G600900 chr2D 651416290 651420296 4006 False 7400.0 7400 100.000 1 4007 1 chr2D.!!$F1 4006
1 TraesCS2D01G600900 chr2D 461294387 461295032 645 True 939.0 939 93.395 3141 3768 1 chr2D.!!$R1 627
2 TraesCS2D01G600900 chr2A 776216335 776219505 3170 True 4475.0 4475 92.361 1 3139 1 chr2A.!!$R1 3138
3 TraesCS2D01G600900 chr2A 776549081 776551068 1987 False 734.5 822 89.961 1830 3010 2 chr2A.!!$F1 1180
4 TraesCS2D01G600900 chr2B 780665839 780667762 1923 True 3040.0 3040 95.233 1097 3017 1 chr2B.!!$R1 1920
5 TraesCS2D01G600900 chr2B 780975567 780977446 1879 False 2481.0 2481 90.328 1217 3139 1 chr2B.!!$F2 1922
6 TraesCS2D01G600900 chr2B 794338685 794339576 891 False 444.0 773 86.202 3143 4007 2 chr2B.!!$F3 864
7 TraesCS2D01G600900 chr1D 493951912 493954054 2142 True 2826.0 2826 90.218 777 3013 1 chr1D.!!$R1 2236
8 TraesCS2D01G600900 chr7A 624965185 624967000 1815 True 1626.0 1626 82.978 1116 2925 1 chr7A.!!$R1 1809
9 TraesCS2D01G600900 chr7B 586659733 586661546 1813 False 1600.0 1600 82.749 1118 2925 1 chr7B.!!$F3 1807
10 TraesCS2D01G600900 chr7B 586263858 586265673 1815 True 1581.0 1581 82.549 1116 2925 1 chr7B.!!$R1 1809
11 TraesCS2D01G600900 chr7B 385621822 385622710 888 False 811.0 811 83.885 3143 4007 1 chr7B.!!$F2 864
12 TraesCS2D01G600900 chr7B 10057025 10057878 853 False 747.0 747 83.295 3143 3973 1 chr7B.!!$F1 830
13 TraesCS2D01G600900 chr7D 543602370 543604188 1818 False 1555.0 1555 82.279 1111 2925 1 chr7D.!!$F1 1814
14 TraesCS2D01G600900 chr7D 543057706 543059521 1815 True 1554.0 1554 82.276 1116 2925 1 chr7D.!!$R1 1809
15 TraesCS2D01G600900 chr5A 505626118 505627933 1815 True 1537.0 1537 82.112 1116 2925 1 chr5A.!!$R1 1809
16 TraesCS2D01G600900 chr1B 559585617 559586525 908 False 1430.0 1430 94.822 1011 1937 1 chr1B.!!$F2 926
17 TraesCS2D01G600900 chr1B 190313968 190314869 901 False 800.0 800 83.696 3143 4007 1 chr1B.!!$F1 864
18 TraesCS2D01G600900 chr1B 484264951 484265836 885 True 769.0 769 83.150 3143 4007 1 chr1B.!!$R1 864

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
246 249 0.034186 TGTCTTCCCCATGCATCCAC 60.034 55.000 0.00 0.00 0.00 4.02 F
806 853 0.316204 ACCGTCCGATCGTGAAAACT 59.684 50.000 15.09 0.00 0.00 2.66 F
906 953 1.372499 GTCACGCCAACGCTGTAGA 60.372 57.895 0.00 0.00 45.53 2.59 F
972 1027 1.477295 ACGTACTTGGAGCTAGCTTCC 59.523 52.381 20.67 20.41 0.00 3.46 F
986 1041 1.478510 AGCTTCCAGACGACATCGATT 59.521 47.619 8.54 0.00 43.02 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1566 0.825840 GATAGGCCTCGGCAGTCTCT 60.826 60.000 9.68 0.0 44.11 3.10 R
1689 1756 2.283676 TTCCGCTCCTTCCCGTCT 60.284 61.111 0.00 0.0 0.00 4.18 R
2973 3896 1.666011 GTCGTTGTCCTCCTCAGCA 59.334 57.895 0.00 0.0 0.00 4.41 R
2976 3899 1.802337 CGTGGTCGTTGTCCTCCTCA 61.802 60.000 0.00 0.0 0.00 3.86 R
3103 4038 6.980397 ACAGACAAACAATCAACAAGATTTCC 59.020 34.615 0.00 0.0 44.48 3.13 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
81 82 5.359576 ACTGAAGAGTTGCTCAGTAGATAGG 59.640 44.000 2.97 0.00 41.08 2.57
94 95 5.536538 TCAGTAGATAGGACAATGTAGCCTG 59.463 44.000 4.10 0.00 33.28 4.85
120 121 0.881118 ATGGCGTGTTTAGCAAGTGG 59.119 50.000 0.00 0.00 36.08 4.00
136 137 0.751643 GTGGCATGCGAATTAGGGGT 60.752 55.000 12.44 0.00 0.00 4.95
139 140 1.202405 GGCATGCGAATTAGGGGTTTG 60.202 52.381 12.44 0.00 0.00 2.93
144 146 3.078837 TGCGAATTAGGGGTTTGTCTTC 58.921 45.455 0.00 0.00 0.00 2.87
146 148 4.020039 TGCGAATTAGGGGTTTGTCTTCTA 60.020 41.667 0.00 0.00 0.00 2.10
147 149 4.331992 GCGAATTAGGGGTTTGTCTTCTAC 59.668 45.833 0.00 0.00 0.00 2.59
174 176 6.013842 AGGTTTAGCAAGTTCAGTATTTGC 57.986 37.500 0.00 0.00 45.64 3.68
196 199 9.757227 TTTGCACTAACAAATTTAACTAATGCT 57.243 25.926 11.43 0.00 34.68 3.79
209 212 3.290710 ACTAATGCTTAGTTGGCCATGG 58.709 45.455 6.09 7.63 43.70 3.66
210 213 0.826062 AATGCTTAGTTGGCCATGGC 59.174 50.000 29.47 29.47 41.06 4.40
220 223 2.599597 GCCATGGCCCATGAGACT 59.400 61.111 27.24 0.00 43.81 3.24
228 231 1.139853 GGCCCATGAGACTAGAGGTTG 59.860 57.143 0.00 0.00 0.00 3.77
243 246 1.106285 GGTTGTCTTCCCCATGCATC 58.894 55.000 0.00 0.00 0.00 3.91
244 247 1.106285 GTTGTCTTCCCCATGCATCC 58.894 55.000 0.00 0.00 0.00 3.51
245 248 0.703488 TTGTCTTCCCCATGCATCCA 59.297 50.000 0.00 0.00 0.00 3.41
246 249 0.034186 TGTCTTCCCCATGCATCCAC 60.034 55.000 0.00 0.00 0.00 4.02
265 268 1.881973 ACGCATGCAGATCAACTTTGT 59.118 42.857 19.57 0.00 0.00 2.83
266 269 2.247637 CGCATGCAGATCAACTTTGTG 58.752 47.619 19.57 0.00 0.00 3.33
288 291 3.057315 GTGAATGGATTCAGTTGTGGGTG 60.057 47.826 2.20 0.00 46.44 4.61
338 341 6.600822 CAGATTTTCCTGAGGATTTTCTAGCA 59.399 38.462 0.04 0.00 36.29 3.49
340 343 3.550437 TCCTGAGGATTTTCTAGCAGC 57.450 47.619 0.00 0.00 0.00 5.25
349 352 1.538047 TTTCTAGCAGCCCTTTGCAG 58.462 50.000 0.52 0.00 46.47 4.41
350 353 0.692476 TTCTAGCAGCCCTTTGCAGA 59.308 50.000 0.52 0.00 46.47 4.26
353 356 1.888512 CTAGCAGCCCTTTGCAGAAAA 59.111 47.619 0.52 0.00 46.47 2.29
354 357 1.345063 AGCAGCCCTTTGCAGAAAAT 58.655 45.000 0.52 0.00 46.47 1.82
357 360 2.224784 GCAGCCCTTTGCAGAAAATTTG 59.775 45.455 0.00 0.00 44.83 2.32
358 361 3.469739 CAGCCCTTTGCAGAAAATTTGT 58.530 40.909 0.00 0.00 44.83 2.83
359 362 3.249080 CAGCCCTTTGCAGAAAATTTGTG 59.751 43.478 0.00 0.00 44.83 3.33
361 364 3.248363 GCCCTTTGCAGAAAATTTGTGTC 59.752 43.478 4.79 0.00 40.77 3.67
366 373 6.480981 CCTTTGCAGAAAATTTGTGTCAAGAT 59.519 34.615 13.68 0.00 0.00 2.40
369 376 8.939201 TTGCAGAAAATTTGTGTCAAGATAAA 57.061 26.923 4.79 0.00 0.00 1.40
391 398 4.362932 TTTGTGTCGTGATTGCAGAAAA 57.637 36.364 0.00 0.00 0.00 2.29
415 422 2.097466 AGTTCGTGAAGTTTGGCTGTTG 59.903 45.455 0.00 0.00 0.00 3.33
426 433 7.768120 TGAAGTTTGGCTGTTGAAATAACAATT 59.232 29.630 0.00 0.00 32.36 2.32
432 439 7.914465 TGGCTGTTGAAATAACAATTTGAAAC 58.086 30.769 2.79 0.00 32.36 2.78
434 441 8.611757 GGCTGTTGAAATAACAATTTGAAACTT 58.388 29.630 2.79 0.00 32.36 2.66
435 442 9.424659 GCTGTTGAAATAACAATTTGAAACTTG 57.575 29.630 2.79 0.00 32.36 3.16
457 464 7.775561 ACTTGTGTGAAATAACCTTCTTTCTCT 59.224 33.333 0.00 0.00 33.50 3.10
502 509 5.010012 GTGGTGTCCTTGAAATTCAGTGATT 59.990 40.000 0.00 0.00 0.00 2.57
504 511 5.241506 GGTGTCCTTGAAATTCAGTGATTCA 59.758 40.000 5.27 5.27 0.00 2.57
512 519 5.352293 TGAAATTCAGTGATTCACTCCATCG 59.648 40.000 16.39 5.63 43.43 3.84
529 537 2.590092 GGCCTCCTGCGTACCATT 59.410 61.111 0.00 0.00 42.61 3.16
530 538 1.819632 GGCCTCCTGCGTACCATTG 60.820 63.158 0.00 0.00 42.61 2.82
545 553 6.961554 GCGTACCATTGAAATTCAAAGTAGAG 59.038 38.462 12.75 13.43 40.12 2.43
568 576 9.750125 AGAGTTGAATCAAAGTTAAATTTGGTC 57.250 29.630 23.72 20.59 39.99 4.02
584 594 5.462530 TTTGGTCAGAAACGAGATGACTA 57.537 39.130 12.12 6.01 42.36 2.59
587 597 3.444388 GGTCAGAAACGAGATGACTACCT 59.556 47.826 12.12 0.00 42.36 3.08
599 609 4.702131 AGATGACTACCTGAATTTTGGTGC 59.298 41.667 11.96 4.37 37.74 5.01
600 610 2.811431 TGACTACCTGAATTTTGGTGCG 59.189 45.455 11.96 6.87 37.74 5.34
601 611 2.159382 ACTACCTGAATTTTGGTGCGG 58.841 47.619 11.96 6.29 37.74 5.69
602 612 2.159382 CTACCTGAATTTTGGTGCGGT 58.841 47.619 11.96 0.00 37.74 5.68
603 613 1.408969 ACCTGAATTTTGGTGCGGTT 58.591 45.000 2.99 0.00 34.90 4.44
604 614 1.760029 ACCTGAATTTTGGTGCGGTTT 59.240 42.857 2.99 0.00 34.90 3.27
605 615 2.134346 CCTGAATTTTGGTGCGGTTTG 58.866 47.619 0.00 0.00 0.00 2.93
606 616 2.223923 CCTGAATTTTGGTGCGGTTTGA 60.224 45.455 0.00 0.00 0.00 2.69
607 617 3.452474 CTGAATTTTGGTGCGGTTTGAA 58.548 40.909 0.00 0.00 0.00 2.69
608 618 3.861840 TGAATTTTGGTGCGGTTTGAAA 58.138 36.364 0.00 0.00 0.00 2.69
610 620 5.601662 TGAATTTTGGTGCGGTTTGAAATA 58.398 33.333 0.00 0.00 0.00 1.40
611 621 5.694006 TGAATTTTGGTGCGGTTTGAAATAG 59.306 36.000 0.00 0.00 0.00 1.73
612 622 4.920640 TTTTGGTGCGGTTTGAAATAGA 57.079 36.364 0.00 0.00 0.00 1.98
614 624 5.461032 TTTGGTGCGGTTTGAAATAGATT 57.539 34.783 0.00 0.00 0.00 2.40
615 625 5.461032 TTGGTGCGGTTTGAAATAGATTT 57.539 34.783 0.00 0.00 0.00 2.17
616 626 4.804108 TGGTGCGGTTTGAAATAGATTTG 58.196 39.130 0.00 0.00 0.00 2.32
617 627 4.520874 TGGTGCGGTTTGAAATAGATTTGA 59.479 37.500 0.00 0.00 0.00 2.69
618 628 5.184864 TGGTGCGGTTTGAAATAGATTTGAT 59.815 36.000 0.00 0.00 0.00 2.57
679 695 1.545582 CATGTAACCTGCAAAGTGGGG 59.454 52.381 0.00 0.00 0.00 4.96
688 704 2.115266 AAAGTGGGGCCAGGAACG 59.885 61.111 4.39 0.00 0.00 3.95
701 746 3.611766 GCCAGGAACGGATTCTTTTTGTC 60.612 47.826 0.00 0.00 34.98 3.18
702 747 3.568007 CCAGGAACGGATTCTTTTTGTCA 59.432 43.478 0.00 0.00 34.98 3.58
703 748 4.037446 CCAGGAACGGATTCTTTTTGTCAA 59.963 41.667 0.00 0.00 34.98 3.18
706 751 6.533367 CAGGAACGGATTCTTTTTGTCAAAAA 59.467 34.615 19.69 19.69 37.99 1.94
715 760 7.462109 TTCTTTTTGTCAAAAACATGATCGG 57.538 32.000 17.56 7.49 37.82 4.18
718 763 5.766150 TTTGTCAAAAACATGATCGGACT 57.234 34.783 0.00 0.00 37.82 3.85
719 764 4.747540 TGTCAAAAACATGATCGGACTG 57.252 40.909 0.00 0.00 31.20 3.51
806 853 0.316204 ACCGTCCGATCGTGAAAACT 59.684 50.000 15.09 0.00 0.00 2.66
896 943 3.215597 ATTCGTCCACGTCACGCCA 62.216 57.895 10.99 2.18 40.80 5.69
897 944 2.702751 ATTCGTCCACGTCACGCCAA 62.703 55.000 10.99 3.17 40.80 4.52
906 953 1.372499 GTCACGCCAACGCTGTAGA 60.372 57.895 0.00 0.00 45.53 2.59
972 1027 1.477295 ACGTACTTGGAGCTAGCTTCC 59.523 52.381 20.67 20.41 0.00 3.46
986 1041 1.478510 AGCTTCCAGACGACATCGATT 59.521 47.619 8.54 0.00 43.02 3.34
2973 3896 4.760047 GGTGGCCATGACGACGCT 62.760 66.667 9.72 0.00 0.00 5.07
3496 4462 8.885494 TTTCAAAAAGTTCATCGGATTTGAAT 57.115 26.923 11.83 0.00 42.72 2.57
3653 4658 8.788813 CGGATTTAGAAAAGTTCATCGATTTTG 58.211 33.333 0.00 0.00 0.00 2.44
3803 4894 9.862585 GAAACATTTCACGCATTTAAGAAAAAT 57.137 25.926 0.00 0.00 37.15 1.82
3857 4948 4.657814 AAACATGGAGAACATAGTGGGT 57.342 40.909 0.00 0.00 37.84 4.51
3921 5042 1.068055 CGAGTGGCGTAGTGGTTAGTT 60.068 52.381 0.00 0.00 34.64 2.24
3931 5052 4.202030 CGTAGTGGTTAGTTGAGGGATCTC 60.202 50.000 0.00 0.00 40.36 2.75
3965 5086 1.026718 GCTGGTTCGATTCCTGGGTG 61.027 60.000 13.05 0.00 0.00 4.61
3984 5106 1.982073 GCGCACACATTCAGTAGCCC 61.982 60.000 0.30 0.00 0.00 5.19
3987 5109 2.014068 GCACACATTCAGTAGCCCTCC 61.014 57.143 0.00 0.00 0.00 4.30
3988 5110 1.556911 CACACATTCAGTAGCCCTCCT 59.443 52.381 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.927767 ACCCCATCTCCTCGTACTCT 59.072 55.000 0.00 0.00 0.00 3.24
81 82 5.449177 GCCATCTAAAACAGGCTACATTGTC 60.449 44.000 0.00 0.00 43.70 3.18
94 95 4.413495 TGCTAAACACGCCATCTAAAAC 57.587 40.909 0.00 0.00 0.00 2.43
106 107 1.701704 GCATGCCACTTGCTAAACAC 58.298 50.000 6.36 0.00 42.00 3.32
120 121 1.476488 ACAAACCCCTAATTCGCATGC 59.524 47.619 7.91 7.91 0.00 4.06
139 140 7.260558 ACTTGCTAAACCTTTTGTAGAAGAC 57.739 36.000 0.00 0.00 0.00 3.01
144 146 7.027778 ACTGAACTTGCTAAACCTTTTGTAG 57.972 36.000 0.00 0.00 0.00 2.74
146 148 5.914898 ACTGAACTTGCTAAACCTTTTGT 57.085 34.783 0.00 0.00 0.00 2.83
147 149 8.755018 CAAATACTGAACTTGCTAAACCTTTTG 58.245 33.333 0.00 0.00 0.00 2.44
158 160 5.757886 TGTTAGTGCAAATACTGAACTTGC 58.242 37.500 0.00 0.00 41.74 4.01
193 196 4.016838 GCCATGGCCAACTAAGCA 57.983 55.556 27.24 0.00 34.56 3.91
204 207 1.347050 CTCTAGTCTCATGGGCCATGG 59.653 57.143 38.66 29.71 41.66 3.66
205 208 1.347050 CCTCTAGTCTCATGGGCCATG 59.653 57.143 35.67 35.67 42.60 3.66
206 209 1.061812 ACCTCTAGTCTCATGGGCCAT 60.062 52.381 14.78 14.78 0.00 4.40
207 210 0.339859 ACCTCTAGTCTCATGGGCCA 59.660 55.000 9.61 9.61 0.00 5.36
208 211 1.139853 CAACCTCTAGTCTCATGGGCC 59.860 57.143 0.00 0.00 0.00 5.80
209 212 1.834263 ACAACCTCTAGTCTCATGGGC 59.166 52.381 0.00 0.00 0.00 5.36
210 213 3.370104 AGACAACCTCTAGTCTCATGGG 58.630 50.000 0.00 0.00 40.96 4.00
211 214 4.142049 GGAAGACAACCTCTAGTCTCATGG 60.142 50.000 0.00 0.00 43.88 3.66
220 223 1.559682 GCATGGGGAAGACAACCTCTA 59.440 52.381 0.00 0.00 0.00 2.43
228 231 1.097547 CGTGGATGCATGGGGAAGAC 61.098 60.000 2.46 0.00 0.00 3.01
243 246 0.806868 AAGTTGATCTGCATGCGTGG 59.193 50.000 14.09 6.00 0.00 4.94
244 247 2.247637 CAAAGTTGATCTGCATGCGTG 58.752 47.619 14.09 8.72 0.00 5.34
245 248 1.881973 ACAAAGTTGATCTGCATGCGT 59.118 42.857 14.09 0.88 0.00 5.24
246 249 2.247637 CACAAAGTTGATCTGCATGCG 58.752 47.619 14.09 8.20 0.00 4.73
265 268 3.156293 CCCACAACTGAATCCATTCACA 58.844 45.455 0.00 0.00 41.51 3.58
266 269 3.057315 CACCCACAACTGAATCCATTCAC 60.057 47.826 0.00 0.00 41.51 3.18
288 291 2.124411 TCCCAGTAGCTAAATCCACCC 58.876 52.381 0.00 0.00 0.00 4.61
338 341 3.118298 ACACAAATTTTCTGCAAAGGGCT 60.118 39.130 0.00 0.00 45.15 5.19
340 343 4.440880 TGACACAAATTTTCTGCAAAGGG 58.559 39.130 0.00 0.00 0.00 3.95
353 356 8.134895 ACGACACAAATTTATCTTGACACAAAT 58.865 29.630 0.00 0.00 0.00 2.32
354 357 7.430793 CACGACACAAATTTATCTTGACACAAA 59.569 33.333 0.00 0.00 0.00 2.83
357 360 6.655062 TCACGACACAAATTTATCTTGACAC 58.345 36.000 0.00 0.00 0.00 3.67
358 361 6.852858 TCACGACACAAATTTATCTTGACA 57.147 33.333 0.00 0.00 0.00 3.58
359 362 7.201266 GCAATCACGACACAAATTTATCTTGAC 60.201 37.037 7.29 0.00 0.00 3.18
361 364 6.581919 TGCAATCACGACACAAATTTATCTTG 59.418 34.615 0.00 0.00 0.00 3.02
366 373 5.681337 TCTGCAATCACGACACAAATTTA 57.319 34.783 0.00 0.00 0.00 1.40
369 376 4.566545 TTTCTGCAATCACGACACAAAT 57.433 36.364 0.00 0.00 0.00 2.32
374 381 3.814842 ACTCATTTTCTGCAATCACGACA 59.185 39.130 0.00 0.00 0.00 4.35
391 398 2.549754 CAGCCAAACTTCACGAACTCAT 59.450 45.455 0.00 0.00 0.00 2.90
426 433 8.062065 AGAAGGTTATTTCACACAAGTTTCAA 57.938 30.769 0.00 0.00 0.00 2.69
432 439 8.159344 AGAGAAAGAAGGTTATTTCACACAAG 57.841 34.615 11.34 0.00 39.99 3.16
434 441 9.436957 GATAGAGAAAGAAGGTTATTTCACACA 57.563 33.333 11.34 0.42 39.99 3.72
435 442 8.884726 GGATAGAGAAAGAAGGTTATTTCACAC 58.115 37.037 11.34 4.08 39.99 3.82
442 449 7.829706 GGTGTTTGGATAGAGAAAGAAGGTTAT 59.170 37.037 0.00 0.00 0.00 1.89
443 450 7.017254 AGGTGTTTGGATAGAGAAAGAAGGTTA 59.983 37.037 0.00 0.00 0.00 2.85
457 464 3.581755 CGTCGAAAGAGGTGTTTGGATA 58.418 45.455 0.00 0.00 43.49 2.59
502 509 2.060383 CAGGAGGCCGATGGAGTGA 61.060 63.158 0.00 0.00 0.00 3.41
504 511 3.474570 GCAGGAGGCCGATGGAGT 61.475 66.667 0.00 0.00 36.11 3.85
512 519 1.819632 CAATGGTACGCAGGAGGCC 60.820 63.158 0.00 0.00 40.31 5.19
545 553 9.528018 TCTGACCAAATTTAACTTTGATTCAAC 57.472 29.630 17.24 5.26 38.17 3.18
554 562 7.562454 TCTCGTTTCTGACCAAATTTAACTT 57.438 32.000 0.00 0.00 0.00 2.66
556 564 7.534239 GTCATCTCGTTTCTGACCAAATTTAAC 59.466 37.037 0.00 0.00 34.55 2.01
568 576 4.703645 TCAGGTAGTCATCTCGTTTCTG 57.296 45.455 0.00 0.00 0.00 3.02
572 582 5.643777 CCAAAATTCAGGTAGTCATCTCGTT 59.356 40.000 0.00 0.00 0.00 3.85
584 594 1.408969 AACCGCACCAAAATTCAGGT 58.591 45.000 0.00 0.00 39.10 4.00
587 597 3.526931 TTCAAACCGCACCAAAATTCA 57.473 38.095 0.00 0.00 0.00 2.57
599 609 8.438676 AGAGGTATCAAATCTATTTCAAACCG 57.561 34.615 0.00 0.00 31.74 4.44
602 612 9.189156 CCCAAGAGGTATCAAATCTATTTCAAA 57.811 33.333 0.00 0.00 0.00 2.69
603 613 8.752005 CCCAAGAGGTATCAAATCTATTTCAA 57.248 34.615 0.00 0.00 0.00 2.69
650 666 9.638239 CACTTTGCAGGTTACATGTATAAATTT 57.362 29.630 6.36 0.00 0.00 1.82
655 671 5.189928 CCCACTTTGCAGGTTACATGTATA 58.810 41.667 6.36 0.00 0.00 1.47
669 685 2.203625 TTCCTGGCCCCACTTTGC 60.204 61.111 0.00 0.00 0.00 3.68
679 695 2.296190 ACAAAAAGAATCCGTTCCTGGC 59.704 45.455 0.00 0.00 34.81 4.85
688 704 8.216453 CGATCATGTTTTTGACAAAAAGAATCC 58.784 33.333 23.11 13.23 42.62 3.01
701 746 4.858935 ACAACAGTCCGATCATGTTTTTG 58.141 39.130 0.00 0.00 35.04 2.44
702 747 5.067153 TCAACAACAGTCCGATCATGTTTTT 59.933 36.000 0.00 0.00 35.04 1.94
703 748 4.578516 TCAACAACAGTCCGATCATGTTTT 59.421 37.500 0.00 0.00 35.04 2.43
706 751 3.067106 GTCAACAACAGTCCGATCATGT 58.933 45.455 0.00 0.00 0.00 3.21
787 834 0.316204 AGTTTTCACGATCGGACGGT 59.684 50.000 20.98 0.00 37.61 4.83
806 853 1.721664 CGAGTCGATCTGGGCCGTTA 61.722 60.000 6.73 0.00 0.00 3.18
842 889 4.778415 CGGTCTGTCCCACGCGAG 62.778 72.222 15.93 4.16 0.00 5.03
896 943 0.896226 GAAGGGAGGTCTACAGCGTT 59.104 55.000 0.00 0.00 0.00 4.84
897 944 1.313812 CGAAGGGAGGTCTACAGCGT 61.314 60.000 0.00 0.00 0.00 5.07
906 953 1.906105 TTTATGGCGCGAAGGGAGGT 61.906 55.000 12.10 0.00 46.37 3.85
1014 1069 3.234630 TAGCCCGAGCAGCAACGTT 62.235 57.895 0.00 0.00 43.56 3.99
1233 1288 2.670148 GGTGAAGGCGACCCAGGAT 61.670 63.158 0.00 0.00 0.00 3.24
1506 1566 0.825840 GATAGGCCTCGGCAGTCTCT 60.826 60.000 9.68 0.00 44.11 3.10
1689 1756 2.283676 TTCCGCTCCTTCCCGTCT 60.284 61.111 0.00 0.00 0.00 4.18
2973 3896 1.666011 GTCGTTGTCCTCCTCAGCA 59.334 57.895 0.00 0.00 0.00 4.41
2976 3899 1.802337 CGTGGTCGTTGTCCTCCTCA 61.802 60.000 0.00 0.00 0.00 3.86
3103 4038 6.980397 ACAGACAAACAATCAACAAGATTTCC 59.020 34.615 0.00 0.00 44.48 3.13
3275 4214 6.496338 ACTTTTCTTCGAAAACAGTGAACT 57.504 33.333 0.00 0.00 0.00 3.01
3921 5042 0.820226 CTCTGTTGCGAGATCCCTCA 59.180 55.000 0.00 0.00 39.39 3.86
3931 5052 1.144565 CCAGCGATCTCTCTGTTGCG 61.145 60.000 0.00 0.00 0.00 4.85
3965 5086 1.425428 GGCTACTGAATGTGTGCGC 59.575 57.895 0.00 0.00 32.84 6.09


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

AutoCloner maintained by Alex Coulton.