Multiple sequence alignment - TraesCS7D01G433300

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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 TraesCS7D01G433300 chr7D 100.000 6746 0 0 1 6746 553225583 553218838 0.000000e+00 12458.0
1 TraesCS7D01G433300 chr7D 95.862 435 18 0 4604 5038 553220908 553220474 0.000000e+00 704.0
2 TraesCS7D01G433300 chr7D 95.862 435 18 0 4676 5110 553220980 553220546 0.000000e+00 704.0
3 TraesCS7D01G433300 chr7B 94.734 6191 205 30 1 6137 599428701 599422578 0.000000e+00 9515.0
4 TraesCS7D01G433300 chr7B 96.782 435 14 0 4676 5110 599424092 599423658 0.000000e+00 726.0
5 TraesCS7D01G433300 chr7B 95.862 435 18 0 4604 5038 599424020 599423586 0.000000e+00 704.0
6 TraesCS7D01G433300 chr7B 95.592 363 16 0 4604 4966 599423948 599423586 3.510000e-162 582.0
7 TraesCS7D01G433300 chr7B 93.642 173 11 0 6143 6315 599422539 599422367 6.710000e-65 259.0
8 TraesCS7D01G433300 chr7A 95.646 4226 123 24 784 4966 638869943 638865736 0.000000e+00 6728.0
9 TraesCS7D01G433300 chr7A 97.297 1295 30 4 4844 6137 638865565 638864275 0.000000e+00 2193.0
10 TraesCS7D01G433300 chr7A 92.050 805 39 6 1 783 638870820 638870019 0.000000e+00 1109.0
11 TraesCS7D01G433300 chr7A 92.605 595 39 2 6139 6728 638864240 638863646 0.000000e+00 850.0
12 TraesCS7D01G433300 chr7A 96.203 474 18 0 4748 5221 638866098 638865625 0.000000e+00 776.0
13 TraesCS7D01G433300 chr7A 97.796 363 8 0 4676 5038 638866098 638865736 1.600000e-175 627.0
14 TraesCS7D01G433300 chr7A 95.000 120 6 0 4991 5110 638865562 638865443 8.930000e-44 189.0
15 TraesCS7D01G433300 chr7A 96.000 75 3 0 5036 5110 638866098 638866024 9.190000e-24 122.0
16 TraesCS7D01G433300 chr7A 97.917 48 1 0 5063 5110 638865562 638865515 4.340000e-12 84.2
17 TraesCS7D01G433300 chr4A 83.390 1168 185 6 3494 4656 208823055 208824218 0.000000e+00 1074.0
18 TraesCS7D01G433300 chr4A 77.744 656 127 11 3547 4197 207979889 207979248 1.060000e-102 385.0
19 TraesCS7D01G433300 chr4D 83.048 1168 191 6 3494 4656 274465201 274466366 0.000000e+00 1053.0
20 TraesCS7D01G433300 chr4D 74.777 896 196 21 3548 4434 286394634 286393760 6.390000e-100 375.0
21 TraesCS7D01G433300 chr4B 83.048 1168 191 6 3494 4656 273619717 273618552 0.000000e+00 1053.0


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 TraesCS7D01G433300 chr7D 553218838 553225583 6745 True 12458.000000 12458 100.000000 1 6746 1 chr7D.!!$R1 6745
1 TraesCS7D01G433300 chr7D 553220474 553220980 506 True 704.000000 704 95.862000 4604 5110 2 chr7D.!!$R2 506
2 TraesCS7D01G433300 chr7B 599422367 599428701 6334 True 4887.000000 9515 94.188000 1 6315 2 chr7B.!!$R1 6314
3 TraesCS7D01G433300 chr7B 599423586 599424092 506 True 670.666667 726 96.078667 4604 5110 3 chr7B.!!$R2 506
4 TraesCS7D01G433300 chr7A 638863646 638869943 6297 True 1803.366667 6728 95.778000 784 6728 6 chr7A.!!$R1 5944
5 TraesCS7D01G433300 chr7A 638865736 638870820 5084 True 619.333333 1109 95.282000 1 5110 3 chr7A.!!$R2 5109
6 TraesCS7D01G433300 chr4A 208823055 208824218 1163 False 1074.000000 1074 83.390000 3494 4656 1 chr4A.!!$F1 1162
7 TraesCS7D01G433300 chr4A 207979248 207979889 641 True 385.000000 385 77.744000 3547 4197 1 chr4A.!!$R1 650
8 TraesCS7D01G433300 chr4D 274465201 274466366 1165 False 1053.000000 1053 83.048000 3494 4656 1 chr4D.!!$F1 1162
9 TraesCS7D01G433300 chr4D 286393760 286394634 874 True 375.000000 375 74.777000 3548 4434 1 chr4D.!!$R1 886
10 TraesCS7D01G433300 chr4B 273618552 273619717 1165 True 1053.000000 1053 83.048000 3494 4656 1 chr4B.!!$R1 1162

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
652 712 0.404426 TCGGTCTTGTGAGAGAGGGA 59.596 55.0 0.0 0.0 31.07 4.20 F
1244 1380 0.034896 GCTATACCGGTCACATGGGG 59.965 60.0 12.4 0.0 0.00 4.96 F
2629 2792 0.107361 CTGCTGCCATCTCCACATCA 60.107 55.0 0.0 0.0 0.00 3.07 F
4022 4200 0.815615 CTAGAGGTTGGCGGATTGGC 60.816 60.0 0.0 0.0 45.12 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 2792 1.660575 CGACAACTTCGGCGACAGT 60.661 57.895 10.16 13.76 44.60 3.55 R
2751 2914 4.141711 ACTTGTTCAAGAAGTAGCTGGTCA 60.142 41.667 17.75 0.00 31.72 4.02 R
4256 4434 0.461548 TCGACCATCTGCATCTGACC 59.538 55.000 0.00 0.00 0.00 4.02 R
5922 6610 0.251341 GCCAACCATCTCCACACCTT 60.251 55.000 0.00 0.00 0.00 3.50 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
139 146 1.942712 CGCTCCACCGCACGTATAC 60.943 63.158 0.00 0.00 0.00 1.47
473 495 2.261361 GCATTGTTTCGCCACCCC 59.739 61.111 0.00 0.00 0.00 4.95
515 537 5.012328 CTTGGAAGCTAGTCCTCGTTATT 57.988 43.478 6.03 0.00 38.62 1.40
523 545 2.354259 AGTCCTCGTTATTCTCGTCGT 58.646 47.619 0.00 0.00 0.00 4.34
541 563 4.376210 CGTCGTGGTTGCGTTTTATCTTTA 60.376 41.667 0.00 0.00 0.00 1.85
543 565 5.731263 GTCGTGGTTGCGTTTTATCTTTATC 59.269 40.000 0.00 0.00 0.00 1.75
593 615 1.340889 TGCCATGAACAACAAGCCTTC 59.659 47.619 0.00 0.00 32.97 3.46
619 663 4.929819 AATGTTTCGGGCAAAGTTTACT 57.070 36.364 0.00 0.00 0.00 2.24
650 710 0.814457 CCTCGGTCTTGTGAGAGAGG 59.186 60.000 0.00 0.00 39.22 3.69
652 712 0.404426 TCGGTCTTGTGAGAGAGGGA 59.596 55.000 0.00 0.00 31.07 4.20
653 713 1.006043 TCGGTCTTGTGAGAGAGGGAT 59.994 52.381 0.00 0.00 31.07 3.85
654 714 1.135915 CGGTCTTGTGAGAGAGGGATG 59.864 57.143 0.00 0.00 31.07 3.51
655 715 1.484240 GGTCTTGTGAGAGAGGGATGG 59.516 57.143 0.00 0.00 31.07 3.51
656 716 2.183679 GTCTTGTGAGAGAGGGATGGT 58.816 52.381 0.00 0.00 31.07 3.55
657 717 2.569404 GTCTTGTGAGAGAGGGATGGTT 59.431 50.000 0.00 0.00 31.07 3.67
658 718 3.008485 GTCTTGTGAGAGAGGGATGGTTT 59.992 47.826 0.00 0.00 31.07 3.27
659 719 4.223032 GTCTTGTGAGAGAGGGATGGTTTA 59.777 45.833 0.00 0.00 31.07 2.01
660 720 4.223032 TCTTGTGAGAGAGGGATGGTTTAC 59.777 45.833 0.00 0.00 0.00 2.01
661 721 3.516586 TGTGAGAGAGGGATGGTTTACA 58.483 45.455 0.00 0.00 0.00 2.41
662 722 4.104086 TGTGAGAGAGGGATGGTTTACAT 58.896 43.478 0.00 0.00 44.18 2.29
663 723 4.080919 TGTGAGAGAGGGATGGTTTACATG 60.081 45.833 0.00 0.00 40.72 3.21
664 724 4.162320 GTGAGAGAGGGATGGTTTACATGA 59.838 45.833 0.00 0.00 40.72 3.07
665 725 4.782691 TGAGAGAGGGATGGTTTACATGAA 59.217 41.667 0.00 0.00 40.72 2.57
666 726 5.104259 AGAGAGGGATGGTTTACATGAAC 57.896 43.478 0.00 0.00 40.72 3.18
667 727 4.536090 AGAGAGGGATGGTTTACATGAACA 59.464 41.667 0.00 0.00 40.72 3.18
700 760 2.109128 TGGGGTTAATGTGGAGCTTTGA 59.891 45.455 0.00 0.00 0.00 2.69
761 821 4.229876 ACACGCGTTAAGTTTCTACCTAC 58.770 43.478 10.22 0.00 0.00 3.18
822 957 7.224557 GCCTGAAATTTTGTATGTGTTCAACTT 59.775 33.333 0.00 0.00 0.00 2.66
861 996 0.519077 CTCGCCAAAGTCCTCAAAGC 59.481 55.000 0.00 0.00 0.00 3.51
1178 1314 2.894387 GCTCATGACCAGCTCGCC 60.894 66.667 0.00 0.00 33.75 5.54
1233 1369 3.655276 ACGATTGGGTTAGCTATACCG 57.345 47.619 14.84 8.49 36.49 4.02
1236 1372 3.613432 CGATTGGGTTAGCTATACCGGTC 60.613 52.174 12.40 0.00 36.49 4.79
1244 1380 0.034896 GCTATACCGGTCACATGGGG 59.965 60.000 12.40 0.00 0.00 4.96
1442 1578 5.532557 TCATGTAGAATCTGGCAGTAATCG 58.467 41.667 15.27 0.00 0.00 3.34
1476 1612 1.373435 CTTGGCCCCGTGTTCTACA 59.627 57.895 0.00 0.00 0.00 2.74
1516 1652 6.882610 TTACTAATAAGCCAATGATGCAGG 57.117 37.500 0.00 0.00 0.00 4.85
1633 1769 4.419522 TTCGGCAAAAATCTAAGTCTGC 57.580 40.909 0.00 0.00 0.00 4.26
1927 2063 3.215975 TGGTTGTTGTAGCTGGTTAACC 58.784 45.455 18.27 18.27 37.27 2.85
1998 2134 2.963782 AGGTTCTGTTAGTCTGACCGTT 59.036 45.455 3.76 0.00 0.00 4.44
1999 2135 3.057734 GGTTCTGTTAGTCTGACCGTTG 58.942 50.000 3.76 0.00 0.00 4.10
2077 2214 4.718940 AGAAAAACTGTGTTTCTGTGGG 57.281 40.909 21.96 0.00 42.38 4.61
2154 2292 7.537715 TGATTGCTAAGTCCAAATTATGTGTG 58.462 34.615 0.00 0.00 0.00 3.82
2333 2472 5.876357 TGGCCAATACTAGTCTCTGTTTTT 58.124 37.500 0.61 0.00 0.00 1.94
2629 2792 0.107361 CTGCTGCCATCTCCACATCA 60.107 55.000 0.00 0.00 0.00 3.07
2726 2889 1.338200 GCTCCCTCAGTGTGTACAAGG 60.338 57.143 0.00 0.00 33.87 3.61
2751 2914 4.891756 CCTGAATGCTAATTGGATTGGTCT 59.108 41.667 0.00 0.00 36.83 3.85
2952 3121 9.482627 AACTGACTCTGTGATCTAGTTTTTAAG 57.517 33.333 0.00 0.00 0.00 1.85
3130 3304 8.417106 TCCTGCTCTTGTTTATAAGTAGATCTG 58.583 37.037 5.18 0.00 0.00 2.90
3208 3383 6.705825 GTGAAAATCAAACCATTTTAGGTGCT 59.294 34.615 0.00 0.00 42.25 4.40
3235 3410 5.176958 GCATTTGGCTATCATGATTTTCTGC 59.823 40.000 14.65 10.27 40.25 4.26
3530 3705 8.883954 TTTCACATGTTGCAGATTTTCAAATA 57.116 26.923 0.00 0.00 0.00 1.40
4022 4200 0.815615 CTAGAGGTTGGCGGATTGGC 60.816 60.000 0.00 0.00 45.12 4.52
4038 4216 4.082026 GGATTGGCCAATGATATTACTGCC 60.082 45.833 35.31 20.74 37.90 4.85
4063 4241 3.063997 GGAAAATGGCTATGACACAGACG 59.936 47.826 0.00 0.00 0.00 4.18
4162 4340 1.734655 AGGACAAGAGCCCTTCAGAA 58.265 50.000 0.00 0.00 0.00 3.02
4256 4434 0.898320 ACTGTCAGTTCATCGGAGGG 59.102 55.000 0.00 0.00 0.00 4.30
4450 4628 3.857052 TCTTCTAATGGCAGTGGTAACG 58.143 45.455 0.00 0.00 42.51 3.18
4861 5404 3.737266 GTCGACGTCATCAAAACCAACTA 59.263 43.478 17.16 0.00 0.00 2.24
4863 5406 4.624024 TCGACGTCATCAAAACCAACTATC 59.376 41.667 17.16 0.00 0.00 2.08
4912 5599 4.889409 TCAAAGAGAAAATCAAGCCACTGT 59.111 37.500 0.00 0.00 0.00 3.55
4917 5604 3.953612 AGAAAATCAAGCCACTGTCAACA 59.046 39.130 0.00 0.00 0.00 3.33
4935 5622 6.042143 GTCAACATCATCAAAACCAACTGTT 58.958 36.000 0.00 0.00 39.43 3.16
4984 5671 3.930634 AAGAGAAAATCAAGCCACTGC 57.069 42.857 0.00 0.00 37.95 4.40
4989 5676 0.681175 AAATCAAGCCACTGCCAACC 59.319 50.000 0.00 0.00 38.69 3.77
5007 5694 4.141959 CCAACCTCATCAAAACCAACTGTT 60.142 41.667 0.00 0.00 39.43 3.16
5032 5719 7.685481 TGGTAATGTTTCTGGTAATTCTCAGA 58.315 34.615 6.57 6.57 38.14 3.27
5075 5762 2.971330 TGCCAACCTCATCAAAACCAAT 59.029 40.909 0.00 0.00 0.00 3.16
5079 5766 4.990426 CCAACCTCATCAAAACCAATTGTC 59.010 41.667 4.43 0.00 0.00 3.18
5111 5798 9.300681 TGTTTCTGGTAATTCTCAGATCAAAAT 57.699 29.630 10.29 0.00 39.42 1.82
5148 5835 3.482783 GAGAAGCCACGCGAGCAC 61.483 66.667 23.58 17.32 0.00 4.40
5346 6033 2.036733 TGGTCAGGTTAAACAGGAGACG 59.963 50.000 0.00 0.00 0.00 4.18
5449 6136 1.660167 CATTTCCAGCAGCGATCAGA 58.340 50.000 0.00 0.00 0.00 3.27
5700 6387 3.374506 GGTTCATACACCTACCGGC 57.625 57.895 0.00 0.00 33.50 6.13
5833 6521 1.131315 GCGAGAACATTTGAGGGCTTC 59.869 52.381 0.00 0.00 0.00 3.86
5922 6610 6.592220 ATATGTAATATAACAATGCGACGGCA 59.408 34.615 0.00 0.00 45.85 5.69
5962 6650 3.851105 GCCGATTGACTATCTTGCAATGC 60.851 47.826 0.00 0.00 32.80 3.56
5983 6671 3.381949 CGCTCCCTCGGTTTCTATTTAG 58.618 50.000 0.00 0.00 0.00 1.85
6053 6741 5.542635 ACTGGTGTAGAAAGAGTTGATACCA 59.457 40.000 0.00 0.00 34.77 3.25
6089 6777 4.259356 ACCAGTTCGCTTTTCTTATACCC 58.741 43.478 0.00 0.00 0.00 3.69
6113 6801 9.176460 CCCGAGGGTTTAATACTTTTTATGTAA 57.824 33.333 0.00 0.00 0.00 2.41
6184 6905 6.514870 GCAAGATTATGCAATTGGTTCGGATA 60.515 38.462 7.72 0.00 45.70 2.59
6281 7003 5.237561 GTCTAGATCGATGTTCTGAGCTGTA 59.762 44.000 0.54 0.00 32.33 2.74
6295 7017 1.633171 CTGTACGATGCGCTCTTGC 59.367 57.895 9.73 1.83 0.00 4.01
6320 7042 5.570344 CACAAAATCTTAGCTGCTCATCAG 58.430 41.667 4.91 0.00 45.62 2.90
6325 7047 4.541973 TCTTAGCTGCTCATCAGTGAAA 57.458 40.909 4.91 0.00 44.66 2.69
6362 7084 3.082579 GCGAGTGGGTGGGCTCTAG 62.083 68.421 0.00 0.00 0.00 2.43
6372 7094 2.565834 GGTGGGCTCTAGGCGATTATTA 59.434 50.000 0.00 0.00 42.94 0.98
6447 7173 0.820871 GTCTAGGAGCACAGGACAGG 59.179 60.000 0.00 0.00 0.00 4.00
6448 7174 0.972983 TCTAGGAGCACAGGACAGGC 60.973 60.000 0.00 0.00 0.00 4.85
6450 7176 4.008933 GGAGCACAGGACAGGCGT 62.009 66.667 0.00 0.00 0.00 5.68
6451 7177 2.646175 GGAGCACAGGACAGGCGTA 61.646 63.158 0.00 0.00 0.00 4.42
6473 7199 7.484975 CGTACTTCTCAGGTTATTGAAGATCT 58.515 38.462 8.32 0.00 39.17 2.75
6474 7200 7.433719 CGTACTTCTCAGGTTATTGAAGATCTG 59.566 40.741 0.00 0.00 39.17 2.90
6476 7202 5.620738 TCTCAGGTTATTGAAGATCTGGG 57.379 43.478 0.00 0.00 0.00 4.45
6494 7220 1.472878 GGGCGTTTCTTTCCTTCCATC 59.527 52.381 0.00 0.00 0.00 3.51
6532 7258 5.104374 GGCATCCATTTGTTGTCAGTAATG 58.896 41.667 0.00 0.00 0.00 1.90
6538 7264 4.418013 TTTGTTGTCAGTAATGGCATCG 57.582 40.909 0.00 0.00 0.00 3.84
6547 7273 2.361119 AGTAATGGCATCGCGAAGAGTA 59.639 45.455 15.24 0.00 0.00 2.59
6552 7278 0.806102 GCATCGCGAAGAGTAAGGCA 60.806 55.000 15.24 0.00 0.00 4.75
6560 7286 2.541556 GAAGAGTAAGGCATCGTCCAC 58.458 52.381 0.00 0.00 0.00 4.02
6688 7414 2.404995 GCAGCAGCACCTGGATCAC 61.405 63.158 0.00 0.00 41.58 3.06
6707 7433 1.300080 CAGGCAGCCCAAACAAACG 60.300 57.895 8.22 0.00 0.00 3.60
6715 7441 4.201970 GCAGCCCAAACAAACGCTATAATA 60.202 41.667 0.00 0.00 0.00 0.98
6728 7454 7.653767 AACGCTATAATATTCTACCAGTTGC 57.346 36.000 0.00 0.00 0.00 4.17
6729 7455 6.994221 ACGCTATAATATTCTACCAGTTGCT 58.006 36.000 0.00 0.00 0.00 3.91
6730 7456 6.868864 ACGCTATAATATTCTACCAGTTGCTG 59.131 38.462 0.00 0.00 0.00 4.41
6731 7457 6.183360 CGCTATAATATTCTACCAGTTGCTGC 60.183 42.308 0.00 0.00 0.00 5.25
6732 7458 6.876257 GCTATAATATTCTACCAGTTGCTGCT 59.124 38.462 0.00 0.00 0.00 4.24
6733 7459 7.389053 GCTATAATATTCTACCAGTTGCTGCTT 59.611 37.037 0.00 0.00 0.00 3.91
6734 7460 7.736447 ATAATATTCTACCAGTTGCTGCTTC 57.264 36.000 0.00 0.00 0.00 3.86
6735 7461 2.928801 TTCTACCAGTTGCTGCTTCA 57.071 45.000 0.00 0.00 0.00 3.02
6736 7462 2.928801 TCTACCAGTTGCTGCTTCAA 57.071 45.000 0.00 0.00 0.00 2.69
6737 7463 3.207265 TCTACCAGTTGCTGCTTCAAA 57.793 42.857 0.00 0.00 0.00 2.69
6738 7464 3.141398 TCTACCAGTTGCTGCTTCAAAG 58.859 45.455 0.00 0.00 0.00 2.77
6739 7465 2.057137 ACCAGTTGCTGCTTCAAAGA 57.943 45.000 0.00 0.00 0.00 2.52
6740 7466 2.590821 ACCAGTTGCTGCTTCAAAGAT 58.409 42.857 0.00 0.00 0.00 2.40
6741 7467 2.555757 ACCAGTTGCTGCTTCAAAGATC 59.444 45.455 0.00 0.00 0.00 2.75
6742 7468 2.818432 CCAGTTGCTGCTTCAAAGATCT 59.182 45.455 0.00 0.00 0.00 2.75
6743 7469 3.119919 CCAGTTGCTGCTTCAAAGATCTC 60.120 47.826 0.00 0.00 0.00 2.75
6744 7470 3.501062 CAGTTGCTGCTTCAAAGATCTCA 59.499 43.478 0.00 0.00 0.00 3.27
6745 7471 4.023450 CAGTTGCTGCTTCAAAGATCTCAA 60.023 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 298 2.693017 GGAGCAGGAGGAGGAGGA 59.307 66.667 0.00 0.00 0.00 3.71
473 495 1.291877 CTTCAGAAAGGCCCACGACG 61.292 60.000 0.00 0.00 0.00 5.12
505 527 1.399440 CCACGACGAGAATAACGAGGA 59.601 52.381 0.00 0.00 38.37 3.71
513 535 0.599204 AACGCAACCACGACGAGAAT 60.599 50.000 0.00 0.00 36.70 2.40
515 537 0.806884 AAAACGCAACCACGACGAGA 60.807 50.000 0.00 0.00 36.70 4.04
523 545 6.811253 ACTGATAAAGATAAAACGCAACCA 57.189 33.333 0.00 0.00 0.00 3.67
541 563 2.216046 CATGCCAGCAACGATACTGAT 58.784 47.619 0.00 0.00 35.90 2.90
543 565 0.659427 CCATGCCAGCAACGATACTG 59.341 55.000 0.00 0.00 0.00 2.74
593 615 1.794116 CTTTGCCCGAAACATTTGCAG 59.206 47.619 0.00 0.00 32.88 4.41
619 663 3.738481 CCGAGGGCCAAATGGGGA 61.738 66.667 6.18 0.00 37.04 4.81
650 710 4.023291 ACCCATGTTCATGTAAACCATCC 58.977 43.478 11.13 0.00 0.00 3.51
652 712 4.322650 GCAACCCATGTTCATGTAAACCAT 60.323 41.667 11.13 0.00 30.42 3.55
653 713 3.006323 GCAACCCATGTTCATGTAAACCA 59.994 43.478 11.13 0.00 30.42 3.67
654 714 3.258123 AGCAACCCATGTTCATGTAAACC 59.742 43.478 11.13 0.00 30.42 3.27
655 715 4.519540 AGCAACCCATGTTCATGTAAAC 57.480 40.909 11.13 0.00 30.42 2.01
656 716 4.832266 AGAAGCAACCCATGTTCATGTAAA 59.168 37.500 11.13 0.00 30.42 2.01
657 717 4.218200 CAGAAGCAACCCATGTTCATGTAA 59.782 41.667 11.13 0.00 30.42 2.41
658 718 3.758023 CAGAAGCAACCCATGTTCATGTA 59.242 43.478 11.13 0.00 30.42 2.29
659 719 2.559668 CAGAAGCAACCCATGTTCATGT 59.440 45.455 11.13 0.00 30.42 3.21
660 720 2.094390 CCAGAAGCAACCCATGTTCATG 60.094 50.000 5.88 5.88 30.42 3.07
661 721 2.173519 CCAGAAGCAACCCATGTTCAT 58.826 47.619 0.00 0.00 30.42 2.57
662 722 1.619654 CCAGAAGCAACCCATGTTCA 58.380 50.000 0.00 0.00 30.42 3.18
663 723 0.890683 CCCAGAAGCAACCCATGTTC 59.109 55.000 0.00 0.00 30.42 3.18
664 724 0.542702 CCCCAGAAGCAACCCATGTT 60.543 55.000 0.00 0.00 34.14 2.71
665 725 1.077265 CCCCAGAAGCAACCCATGT 59.923 57.895 0.00 0.00 0.00 3.21
666 726 0.542702 AACCCCAGAAGCAACCCATG 60.543 55.000 0.00 0.00 0.00 3.66
667 727 1.080638 TAACCCCAGAAGCAACCCAT 58.919 50.000 0.00 0.00 0.00 4.00
712 772 6.952935 AACATCGAGCAACTTTAGTAGAAG 57.047 37.500 0.00 0.00 0.00 2.85
761 821 6.272318 TCCACAAGAAAGTAGCAAACATTTG 58.728 36.000 0.00 0.00 41.03 2.32
822 957 6.183360 GGCGAGAGAAAACCGATATTACAAAA 60.183 38.462 0.00 0.00 0.00 2.44
826 961 4.365723 TGGCGAGAGAAAACCGATATTAC 58.634 43.478 0.00 0.00 0.00 1.89
834 969 1.535896 GGACTTTGGCGAGAGAAAACC 59.464 52.381 0.00 0.00 0.00 3.27
861 996 0.372334 GGTGCACCGTTAACATAGCG 59.628 55.000 22.49 0.00 0.00 4.26
901 1036 7.544566 CACCGACATTAGTAACTAAGTTGACAT 59.455 37.037 0.00 0.00 29.02 3.06
1178 1314 2.185350 CAGGTAGCACGCCTCCAG 59.815 66.667 0.00 0.00 33.31 3.86
1183 1319 0.887387 TCAAAACCAGGTAGCACGCC 60.887 55.000 0.00 0.00 0.00 5.68
1244 1380 2.298163 TCCTTACGGACTTCACTTGGTC 59.702 50.000 0.00 0.00 33.30 4.02
1442 1578 0.445436 CAAGTTCTCGGCATGTGCTC 59.555 55.000 4.84 0.00 41.70 4.26
1476 1612 6.969993 TTAGTAAAATTGTGGCCTTCTTGT 57.030 33.333 3.32 0.00 0.00 3.16
1511 1647 2.042842 TGATCAATTTCCCCTTCCTGCA 59.957 45.455 0.00 0.00 0.00 4.41
1516 1652 7.653311 CGGAATAAATTGATCAATTTCCCCTTC 59.347 37.037 37.32 30.96 44.98 3.46
1633 1769 2.224523 TGTTACCAAGGAACCTGCTCAG 60.225 50.000 0.00 0.00 0.00 3.35
1927 2063 7.443272 TCATGCTGAGTCATTCCATAAGTATTG 59.557 37.037 0.00 0.00 0.00 1.90
2118 2256 7.894708 TGGACTTAGCAATCATTCATTTGAAA 58.105 30.769 0.00 0.00 37.61 2.69
2125 2263 8.970020 ACATAATTTGGACTTAGCAATCATTCA 58.030 29.630 0.00 0.00 0.00 2.57
2132 2270 5.476599 AGCACACATAATTTGGACTTAGCAA 59.523 36.000 0.00 0.00 0.00 3.91
2154 2292 7.162082 AGCCCTACACTATAATATTCAACAGC 58.838 38.462 0.00 0.00 0.00 4.40
2302 2441 4.222145 AGACTAGTATTGGCCAAGTTTCGA 59.778 41.667 24.94 9.05 0.00 3.71
2333 2472 2.620234 CCTGCCCTGGGATCACTAA 58.380 57.895 19.27 0.00 0.00 2.24
2629 2792 1.660575 CGACAACTTCGGCGACAGT 60.661 57.895 10.16 13.76 44.60 3.55
2726 2889 4.646492 ACCAATCCAATTAGCATTCAGGTC 59.354 41.667 0.00 0.00 0.00 3.85
2751 2914 4.141711 ACTTGTTCAAGAAGTAGCTGGTCA 60.142 41.667 17.75 0.00 31.72 4.02
2952 3121 5.948992 AAGTTCAAACCAGAGAGCATAAC 57.051 39.130 0.00 0.00 0.00 1.89
3061 3230 9.725019 AATATCAACAGTGTTATTCTGAACAGA 57.275 29.630 8.49 0.00 39.93 3.41
3208 3383 6.322969 AGAAAATCATGATAGCCAAATGCAGA 59.677 34.615 9.04 0.00 44.83 4.26
3235 3410 8.905103 TTTTCAGAAAAACCTAGAAAAGAACG 57.095 30.769 5.81 0.00 34.40 3.95
3530 3705 5.964958 AGATGTTTGTCCATCGTTGAAAT 57.035 34.783 0.00 0.00 44.76 2.17
4022 4200 4.271696 TCCTCGGCAGTAATATCATTGG 57.728 45.455 0.00 0.00 0.00 3.16
4030 4208 2.024414 GCCATTTTCCTCGGCAGTAAT 58.976 47.619 0.00 0.00 45.52 1.89
4038 4216 3.270027 TGTGTCATAGCCATTTTCCTCG 58.730 45.455 0.00 0.00 0.00 4.63
4063 4241 9.143631 CAAAGGATCATCTTGGTTATTTTTCAC 57.856 33.333 0.00 0.00 0.00 3.18
4162 4340 3.181423 GGTAGTCTCCTCATCTCCCTGAT 60.181 52.174 0.00 0.00 35.40 2.90
4256 4434 0.461548 TCGACCATCTGCATCTGACC 59.538 55.000 0.00 0.00 0.00 4.02
4600 4778 5.127682 ACAGTGGCTTGATTTTCTCTTTTGT 59.872 36.000 0.00 0.00 0.00 2.83
4861 5404 5.745227 AGAATTACCAGAAACATCACCGAT 58.255 37.500 0.00 0.00 0.00 4.18
4863 5406 4.935205 TGAGAATTACCAGAAACATCACCG 59.065 41.667 0.00 0.00 0.00 4.94
4912 5599 5.850557 ACAGTTGGTTTTGATGATGTTGA 57.149 34.783 0.00 0.00 0.00 3.18
4935 5622 5.875224 TGAGAATTACCAGAAACATCACCA 58.125 37.500 0.00 0.00 0.00 4.17
4984 5671 3.384467 ACAGTTGGTTTTGATGAGGTTGG 59.616 43.478 0.00 0.00 0.00 3.77
5007 5694 7.685481 TCTGAGAATTACCAGAAACATTACCA 58.315 34.615 6.76 0.00 36.58 3.25
5011 5698 8.868522 TTGATCTGAGAATTACCAGAAACATT 57.131 30.769 11.75 0.00 42.02 2.71
5032 5719 5.566230 GCAGTGGCTTGATTTTCTCTTTGAT 60.566 40.000 0.00 0.00 36.96 2.57
5075 5762 2.631160 ACCAGAAACATCACCGACAA 57.369 45.000 0.00 0.00 0.00 3.18
5079 5766 4.935205 TGAGAATTACCAGAAACATCACCG 59.065 41.667 0.00 0.00 0.00 4.94
5111 5798 2.064434 TGTGGAACATCTTGCAACCA 57.936 45.000 0.00 0.00 45.67 3.67
5148 5835 3.067106 AGTGTTTGATGCACCTCTTACG 58.933 45.455 0.00 0.00 37.56 3.18
5149 5836 4.319177 AGAGTGTTTGATGCACCTCTTAC 58.681 43.478 0.00 0.00 37.56 2.34
5346 6033 1.945394 CCTGTCATGCTATCAAGTGGC 59.055 52.381 0.00 0.00 34.40 5.01
5449 6136 1.333177 GCTACCTCTGGATCACGGAT 58.667 55.000 0.00 0.00 33.01 4.18
5700 6387 0.948623 TGGATTTGTCGGTGTCGCTG 60.949 55.000 0.00 0.00 36.13 5.18
5833 6521 1.467713 GGCGTCTCTAGTTGAAGTCGG 60.468 57.143 0.00 0.00 0.00 4.79
5918 6606 1.746615 CCATCTCCACACCTTGCCG 60.747 63.158 0.00 0.00 0.00 5.69
5922 6610 0.251341 GCCAACCATCTCCACACCTT 60.251 55.000 0.00 0.00 0.00 3.50
5926 6614 1.561769 ATCGGCCAACCATCTCCACA 61.562 55.000 2.24 0.00 34.57 4.17
5928 6616 0.394216 CAATCGGCCAACCATCTCCA 60.394 55.000 2.24 0.00 34.57 3.86
5962 6650 2.311124 AAATAGAAACCGAGGGAGCG 57.689 50.000 0.00 0.00 0.00 5.03
5983 6671 1.167851 TGGCATACAAGTCTGCAAGC 58.832 50.000 11.81 0.00 40.18 4.01
6053 6741 4.389374 CGAACTGGTCAATAGCCCAATAT 58.611 43.478 0.00 0.00 0.00 1.28
6174 6895 4.775780 CCATATAGAAGGGTATCCGAACCA 59.224 45.833 4.32 0.00 41.67 3.67
6295 7017 2.160219 TGAGCAGCTAAGATTTTGTGCG 59.840 45.455 0.00 0.00 36.04 5.34
6325 7047 8.894731 CCACTCGCTGTTATAGTACTATATGAT 58.105 37.037 20.67 2.14 0.00 2.45
6356 7078 5.808030 GTCTCCATTAATAATCGCCTAGAGC 59.192 44.000 0.00 0.00 38.52 4.09
6362 7084 7.667043 TGTATTGTCTCCATTAATAATCGCC 57.333 36.000 0.00 0.00 0.00 5.54
6372 7094 6.814954 ACCTACTCATGTATTGTCTCCATT 57.185 37.500 0.00 0.00 0.00 3.16
6447 7173 5.408356 TCTTCAATAACCTGAGAAGTACGC 58.592 41.667 0.00 0.00 38.78 4.42
6448 7174 7.433719 CAGATCTTCAATAACCTGAGAAGTACG 59.566 40.741 0.00 0.00 38.78 3.67
6450 7176 7.147655 CCCAGATCTTCAATAACCTGAGAAGTA 60.148 40.741 0.00 0.00 38.78 2.24
6451 7177 6.352565 CCCAGATCTTCAATAACCTGAGAAGT 60.353 42.308 0.00 0.00 38.78 3.01
6473 7199 0.183971 TGGAAGGAAAGAAACGCCCA 59.816 50.000 0.00 0.00 0.00 5.36
6474 7200 1.472878 GATGGAAGGAAAGAAACGCCC 59.527 52.381 0.00 0.00 0.00 6.13
6476 7202 1.465856 GCGATGGAAGGAAAGAAACGC 60.466 52.381 0.00 0.00 37.11 4.84
6532 7258 1.491505 GCCTTACTCTTCGCGATGCC 61.492 60.000 10.88 0.00 0.00 4.40
6538 7264 1.201343 GACGATGCCTTACTCTTCGC 58.799 55.000 0.00 0.00 35.40 4.70
6547 7273 0.322816 ATTGCAGTGGACGATGCCTT 60.323 50.000 0.00 0.00 41.85 4.35
6552 7278 0.806868 CAAGCATTGCAGTGGACGAT 59.193 50.000 11.53 0.00 40.39 3.73
6606 7332 1.306997 TCCTTCCGGGGCTCTCATT 60.307 57.895 0.00 0.00 35.33 2.57
6688 7414 1.069596 GTTTGTTTGGGCTGCCTGG 59.930 57.895 19.68 0.00 0.00 4.45
6692 7418 0.243636 ATAGCGTTTGTTTGGGCTGC 59.756 50.000 0.00 0.00 36.97 5.25
6707 7433 6.876257 AGCAGCAACTGGTAGAATATTATAGC 59.124 38.462 11.46 11.46 40.59 2.97
6715 7441 3.423539 TGAAGCAGCAACTGGTAGAAT 57.576 42.857 0.00 0.00 41.59 2.40


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

AutoCloner maintained by Alex Coulton.