Multiple sequence alignment - TraesCS5A01G429900

Loading Multiple Alignment...

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 TraesCS5A01G429900 chr5A 100.000 2310 0 0 1 2310 613936187 613933878 0.000000e+00 4266.0
1 TraesCS5A01G429900 chr5A 93.099 797 49 1 813 1609 614228434 614227644 0.000000e+00 1162.0
2 TraesCS5A01G429900 chr5A 100.000 570 0 0 2597 3166 613933591 613933022 0.000000e+00 1053.0
3 TraesCS5A01G429900 chr5D 88.675 1510 99 28 813 2310 491669483 491668034 0.000000e+00 1775.0
4 TraesCS5A01G429900 chr5D 83.041 513 68 8 1063 1566 491660611 491660109 6.230000e-122 448.0
5 TraesCS5A01G429900 chr5D 80.833 360 38 13 2827 3166 491666248 491665900 1.460000e-63 254.0
6 TraesCS5A01G429900 chr5B 94.020 903 43 6 708 1609 606589245 606588353 0.000000e+00 1358.0
7 TraesCS5A01G429900 chr5B 93.672 806 40 5 813 1609 606596682 606595879 0.000000e+00 1195.0
8 TraesCS5A01G429900 chr5B 92.916 607 40 3 1703 2307 606587863 606587258 0.000000e+00 880.0
9 TraesCS5A01G429900 chr5B 85.014 714 96 10 1 708 606589991 606589283 0.000000e+00 715.0
10 TraesCS5A01G429900 chr5B 87.234 376 22 6 2815 3166 606551848 606551475 3.800000e-109 405.0
11 TraesCS5A01G429900 chr5B 89.862 217 16 5 2601 2814 606587221 606587008 1.120000e-69 274.0
12 TraesCS5A01G429900 chr5B 75.000 376 48 19 893 1260 606485439 606485102 7.130000e-27 132.0
13 TraesCS5A01G429900 chr2A 81.034 290 51 4 1764 2050 284125396 284125108 8.830000e-56 228.0
14 TraesCS5A01G429900 chr2D 77.273 220 40 6 482 692 523618961 523619179 1.540000e-23 121.0
15 TraesCS5A01G429900 chr4D 90.741 54 4 1 1 54 287539595 287539543 1.580000e-08 71.3
16 TraesCS5A01G429900 chr2B 100.000 28 0 0 3136 3163 158755370 158755397 6.000000e-03 52.8
17 TraesCS5A01G429900 chr1A 100.000 28 0 0 3136 3163 481151430 481151457 6.000000e-03 52.8


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 TraesCS5A01G429900 chr5A 613933022 613936187 3165 True 2659.50 4266 100.000 1 3166 2 chr5A.!!$R2 3165
1 TraesCS5A01G429900 chr5A 614227644 614228434 790 True 1162.00 1162 93.099 813 1609 1 chr5A.!!$R1 796
2 TraesCS5A01G429900 chr5D 491665900 491669483 3583 True 1014.50 1775 84.754 813 3166 2 chr5D.!!$R2 2353
3 TraesCS5A01G429900 chr5D 491660109 491660611 502 True 448.00 448 83.041 1063 1566 1 chr5D.!!$R1 503
4 TraesCS5A01G429900 chr5B 606595879 606596682 803 True 1195.00 1195 93.672 813 1609 1 chr5B.!!$R3 796
5 TraesCS5A01G429900 chr5B 606587008 606589991 2983 True 806.75 1358 90.453 1 2814 4 chr5B.!!$R4 2813

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
463 468 0.031585 GGGTCGGTTGCTTTCCAAAC 59.968 55.0 0.00 0.00 37.79 2.93 F
703 710 0.176680 AACAGCTGGCCTCGATACTG 59.823 55.0 19.93 5.04 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 2055 0.326264 ATGGCCGGCTTCATATCCTC 59.674 55.000 28.56 5.64 0.00 3.71 R
2623 3105 1.272147 ACTCCCAAGCTTCATGGAACC 60.272 52.381 4.39 0.00 40.56 3.62 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
23 24 2.359850 GTCAGGCCCGCATGTCAA 60.360 61.111 0.00 0.00 0.00 3.18
51 52 4.736793 GGAGCAAATAATCAAAGCGACATG 59.263 41.667 0.00 0.00 0.00 3.21
55 56 6.308766 AGCAAATAATCAAAGCGACATGTTTC 59.691 34.615 0.00 0.00 0.00 2.78
66 67 6.422776 AGCGACATGTTTCGAAGAAATAAT 57.577 33.333 10.81 0.00 45.90 1.28
81 82 5.332743 AGAAATAATTCAAAGCCACCCAGA 58.667 37.500 0.00 0.00 38.06 3.86
84 85 8.302595 GAAATAATTCAAAGCCACCCAGAGGG 62.303 46.154 0.00 0.00 41.13 4.30
102 105 1.219393 GGAGAGGAAGAACAGGCCG 59.781 63.158 0.00 0.00 0.00 6.13
119 122 3.002371 GAGGGGGAAGAAGGGCTG 58.998 66.667 0.00 0.00 0.00 4.85
132 135 4.400961 GGCTGCTCCCTTCGCTGT 62.401 66.667 0.00 0.00 0.00 4.40
134 137 2.507992 CTGCTCCCTTCGCTGTCG 60.508 66.667 0.00 0.00 0.00 4.35
167 170 4.351054 CAACCCTGGCCGCTCCTT 62.351 66.667 0.00 0.00 35.26 3.36
184 187 1.842381 CTTCGGCCCACCTCCTTCTT 61.842 60.000 0.00 0.00 0.00 2.52
207 210 2.948840 CTACCTTTCTACGCCCGCCG 62.949 65.000 0.00 0.00 44.21 6.46
256 259 4.025401 GGCCACGTGCGGACAAAG 62.025 66.667 10.91 0.00 42.61 2.77
280 283 3.545124 AACGCGACTCCCATTGGCA 62.545 57.895 15.93 0.00 0.00 4.92
402 405 2.746277 GACGGCGGCAACTCCATT 60.746 61.111 8.47 0.00 43.61 3.16
403 406 1.448893 GACGGCGGCAACTCCATTA 60.449 57.895 8.47 0.00 43.61 1.90
404 407 1.702491 GACGGCGGCAACTCCATTAC 61.702 60.000 8.47 0.00 43.61 1.89
415 420 5.220796 GGCAACTCCATTACCGAGATTTAAC 60.221 44.000 0.00 0.00 34.01 2.01
417 422 5.334724 ACTCCATTACCGAGATTTAACGT 57.665 39.130 0.00 0.00 0.00 3.99
423 428 6.479001 CCATTACCGAGATTTAACGTCAGATT 59.521 38.462 0.00 0.00 0.00 2.40
424 429 6.880822 TTACCGAGATTTAACGTCAGATTG 57.119 37.500 0.00 0.00 0.00 2.67
458 463 1.002773 TCTAAGGGGTCGGTTGCTTTC 59.997 52.381 0.00 0.00 0.00 2.62
459 464 0.037160 TAAGGGGTCGGTTGCTTTCC 59.963 55.000 0.00 0.00 0.00 3.13
463 468 0.031585 GGGTCGGTTGCTTTCCAAAC 59.968 55.000 0.00 0.00 37.79 2.93
474 479 4.059511 TGCTTTCCAAACATGATTGCAAG 58.940 39.130 10.05 13.54 0.00 4.01
480 485 3.196039 CCAAACATGATTGCAAGGATCCA 59.804 43.478 15.82 0.00 0.00 3.41
482 487 5.424757 CAAACATGATTGCAAGGATCCAAT 58.575 37.500 15.82 4.48 34.57 3.16
484 489 5.018539 ACATGATTGCAAGGATCCAATTG 57.981 39.130 15.82 11.86 32.20 2.32
509 515 8.261522 TGCTTTTTAAAATGTTTGTAAGGACCT 58.738 29.630 13.53 0.00 0.00 3.85
597 603 1.173913 GGCCCCACATGTCAGTTAAC 58.826 55.000 0.00 0.00 0.00 2.01
598 604 1.173913 GCCCCACATGTCAGTTAACC 58.826 55.000 0.88 0.00 0.00 2.85
611 617 5.888724 TGTCAGTTAACCCTCAAACAATCAA 59.111 36.000 0.88 0.00 0.00 2.57
621 627 7.004086 ACCCTCAAACAATCAATTCTCTTACA 58.996 34.615 0.00 0.00 0.00 2.41
625 631 7.884257 TCAAACAATCAATTCTCTTACATGCA 58.116 30.769 0.00 0.00 0.00 3.96
631 637 0.991146 TTCTCTTACATGCAGCCCCA 59.009 50.000 0.00 0.00 0.00 4.96
632 638 0.543277 TCTCTTACATGCAGCCCCAG 59.457 55.000 0.00 0.00 0.00 4.45
633 639 0.254178 CTCTTACATGCAGCCCCAGT 59.746 55.000 0.00 0.00 0.00 4.00
646 653 4.269183 CAGCCCCAGTTGTTATAATCACA 58.731 43.478 0.00 0.00 0.00 3.58
702 709 0.905357 AAACAGCTGGCCTCGATACT 59.095 50.000 19.93 0.00 0.00 2.12
703 710 0.176680 AACAGCTGGCCTCGATACTG 59.823 55.000 19.93 5.04 0.00 2.74
708 715 0.962489 CTGGCCTCGATACTGGTAGG 59.038 60.000 3.32 0.00 0.00 3.18
709 716 0.554305 TGGCCTCGATACTGGTAGGA 59.446 55.000 3.32 0.00 0.00 2.94
716 762 1.687123 CGATACTGGTAGGAACCCTGG 59.313 57.143 0.00 0.00 46.16 4.45
739 785 6.603997 TGGCCCGAATTGTAATAGTTTTATGT 59.396 34.615 0.00 0.00 0.00 2.29
763 809 4.868450 TTTACTTCACGAACTGTTGTGG 57.132 40.909 17.08 9.05 36.74 4.17
772 818 1.476488 GAACTGTTGTGGGTTGCACTT 59.524 47.619 0.00 0.00 0.00 3.16
773 819 1.555967 ACTGTTGTGGGTTGCACTTT 58.444 45.000 0.00 0.00 0.00 2.66
783 829 2.687935 GGGTTGCACTTTGAGAAGTTGA 59.312 45.455 0.00 0.00 43.48 3.18
858 904 6.831353 TCTTTGTGAGGAATTAACACCAAGAA 59.169 34.615 15.99 6.88 40.58 2.52
1038 1084 1.480789 TTCCCTCGATTCCGACATCA 58.519 50.000 0.00 0.00 40.30 3.07
1049 1095 1.080501 CGACATCACTCCACACGCT 60.081 57.895 0.00 0.00 0.00 5.07
1122 1174 2.586293 GCAAACAGCAATGGCCCCT 61.586 57.895 0.00 0.00 44.79 4.79
1155 1207 3.567797 GCCTTCACGCTCATCGCC 61.568 66.667 0.00 0.00 43.23 5.54
1214 1277 0.322636 ACCGCGATATCGATCCCTCT 60.323 55.000 28.63 0.07 43.02 3.69
1567 1639 2.767445 CCGTGATAGCCGGTCGTGA 61.767 63.158 1.90 0.00 40.59 4.35
1568 1640 1.585521 CGTGATAGCCGGTCGTGAC 60.586 63.158 1.90 0.00 0.00 3.67
1606 1678 7.928307 TCTGAAAACTGAGAATAATTCAGGG 57.072 36.000 11.95 0.00 42.36 4.45
1631 2006 5.412594 TCTGTTTGCACTGATATTTCTGTCC 59.587 40.000 0.00 0.00 32.29 4.02
1680 2055 5.617609 TCGAAGAAAAGACGCAATACAATG 58.382 37.500 0.00 0.00 0.00 2.82
1710 2179 4.714802 TGAAGCCGGCCATACAGTATATAT 59.285 41.667 26.15 0.00 0.00 0.86
1778 2247 6.773976 TGATTTATAGGGCCTCTTTGTTTG 57.226 37.500 10.74 0.00 0.00 2.93
1817 2286 9.480053 AAATGCATAAATAGGAAACATGTATGC 57.520 29.630 14.57 14.57 41.60 3.14
1828 2297 4.989279 AACATGTATGCTTGGAATGACC 57.011 40.909 0.00 0.00 39.54 4.02
1853 2322 9.211485 CCTGCCAATTGGATTATTATGAATTTC 57.789 33.333 29.02 4.72 37.39 2.17
1914 2392 2.832838 TCCAAGAGGCTGGAGTGAATA 58.167 47.619 0.00 0.00 40.71 1.75
1916 2394 2.237143 CCAAGAGGCTGGAGTGAATACA 59.763 50.000 0.00 0.00 38.96 2.29
1918 2396 3.902881 AGAGGCTGGAGTGAATACAAG 57.097 47.619 0.00 0.00 0.00 3.16
1949 2428 7.823310 CCCATGAAATGTTGTAAAATGAATCCA 59.177 33.333 0.00 0.00 44.81 3.41
1996 2475 1.916000 CCTACGAATCGAACGACCAAC 59.084 52.381 10.55 0.00 34.70 3.77
2050 2529 9.672673 CCTTGAGAACTCTTATGAAAATCCTTA 57.327 33.333 3.51 0.00 0.00 2.69
2085 2564 4.778534 TCTATTATACCACGCTGCTACC 57.221 45.455 0.00 0.00 0.00 3.18
2094 2573 2.126071 GCTGCTACCGCGACAGAA 60.126 61.111 8.23 0.00 39.65 3.02
2645 3127 3.561313 GGTTCCATGAAGCTTGGGAGTAA 60.561 47.826 2.10 0.00 37.13 2.24
2646 3128 3.634397 TCCATGAAGCTTGGGAGTAAG 57.366 47.619 2.10 0.00 34.85 2.34
2652 3134 5.241403 TGAAGCTTGGGAGTAAGAAATCA 57.759 39.130 2.10 0.00 0.00 2.57
2658 3140 4.137116 TGGGAGTAAGAAATCATCACCG 57.863 45.455 0.00 0.00 0.00 4.94
2734 3218 2.482336 GCGGTCACATGTTTGTCATACA 59.518 45.455 0.00 0.00 34.67 2.29
2735 3219 3.424829 GCGGTCACATGTTTGTCATACAG 60.425 47.826 0.00 0.00 34.67 2.74
2736 3220 3.993736 CGGTCACATGTTTGTCATACAGA 59.006 43.478 0.00 0.00 34.67 3.41
2737 3221 4.631377 CGGTCACATGTTTGTCATACAGAT 59.369 41.667 0.00 0.00 34.67 2.90
2750 3234 9.489084 TTTGTCATACAGATATATACTTGCCAC 57.511 33.333 0.00 0.00 0.00 5.01
2770 3254 2.030451 ACCGACCGACAGAGAAAAGTAC 60.030 50.000 0.00 0.00 0.00 2.73
2805 3289 0.546747 ACCACCTCCGATTCAAGGGA 60.547 55.000 6.95 0.00 36.95 4.20
2812 3296 3.356290 CTCCGATTCAAGGGACCAAAAT 58.644 45.455 0.00 0.00 0.00 1.82
2820 4827 7.255590 CGATTCAAGGGACCAAAATTATATGCT 60.256 37.037 0.00 0.00 0.00 3.79
2821 4828 7.732222 TTCAAGGGACCAAAATTATATGCTT 57.268 32.000 0.00 0.00 0.00 3.91
2823 4830 6.098124 TCAAGGGACCAAAATTATATGCTTGG 59.902 38.462 3.30 3.30 43.33 3.61
2825 4832 4.298332 GGACCAAAATTATATGCTTGGCG 58.702 43.478 4.56 0.00 41.75 5.69
2834 4841 3.715628 ATATGCTTGGCGATGGAAAAC 57.284 42.857 0.00 0.00 0.00 2.43
2835 4842 1.549203 ATGCTTGGCGATGGAAAACT 58.451 45.000 0.00 0.00 0.00 2.66
2836 4843 1.327303 TGCTTGGCGATGGAAAACTT 58.673 45.000 0.00 0.00 0.00 2.66
2946 4970 6.872628 TTTGCAATTCATTTAAATGGCACA 57.127 29.167 24.40 16.62 43.56 4.57
2986 5010 1.599071 CGTGCTTGCTTGTTCTTCTCA 59.401 47.619 0.00 0.00 0.00 3.27
2992 5016 5.750067 TGCTTGCTTGTTCTTCTCATTTTTC 59.250 36.000 0.00 0.00 0.00 2.29
2993 5017 5.108103 GCTTGCTTGTTCTTCTCATTTTTCG 60.108 40.000 0.00 0.00 0.00 3.46
2996 5020 5.238432 TGCTTGTTCTTCTCATTTTTCGCTA 59.762 36.000 0.00 0.00 0.00 4.26
3001 5025 9.773328 TTGTTCTTCTCATTTTTCGCTAATATG 57.227 29.630 0.00 0.00 0.00 1.78
3011 5035 9.311916 CATTTTTCGCTAATATGGGAAATTTGA 57.688 29.630 0.00 0.00 44.38 2.69
3059 5085 8.479313 ACAATGTCCTGAAAAGAAAAGAAAAC 57.521 30.769 0.00 0.00 0.00 2.43
3060 5086 8.093927 ACAATGTCCTGAAAAGAAAAGAAAACA 58.906 29.630 0.00 0.00 0.00 2.83
3061 5087 8.382875 CAATGTCCTGAAAAGAAAAGAAAACAC 58.617 33.333 0.00 0.00 0.00 3.32
3063 5089 8.343168 TGTCCTGAAAAGAAAAGAAAACACTA 57.657 30.769 0.00 0.00 0.00 2.74
3064 5090 8.966868 TGTCCTGAAAAGAAAAGAAAACACTAT 58.033 29.630 0.00 0.00 0.00 2.12
3065 5091 9.237846 GTCCTGAAAAGAAAAGAAAACACTATG 57.762 33.333 0.00 0.00 0.00 2.23
3066 5092 8.966868 TCCTGAAAAGAAAAGAAAACACTATGT 58.033 29.630 0.00 0.00 0.00 2.29
3067 5093 9.237846 CCTGAAAAGAAAAGAAAACACTATGTC 57.762 33.333 0.00 0.00 0.00 3.06
3068 5094 9.787532 CTGAAAAGAAAAGAAAACACTATGTCA 57.212 29.630 0.00 0.00 0.00 3.58
3134 5160 7.455641 TTTTAATGGTCGGTGTTAACATGAT 57.544 32.000 12.26 1.43 0.00 2.45
3139 5165 8.740123 AATGGTCGGTGTTAACATGATATAAA 57.260 30.769 12.26 0.00 0.00 1.40
3140 5166 8.740123 ATGGTCGGTGTTAACATGATATAAAA 57.260 30.769 12.26 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.451927 GATTGACATGCGGGCCTGA 60.452 57.895 18.31 0.05 0.00 3.86
9 10 1.228228 ATGATTGACATGCGGGCCT 59.772 52.632 0.84 0.00 37.87 5.19
23 24 5.300034 TCGCTTTGATTATTTGCTCCATGAT 59.700 36.000 0.00 0.00 0.00 2.45
51 52 7.148804 GGTGGCTTTGAATTATTTCTTCGAAAC 60.149 37.037 0.00 0.00 32.78 2.78
55 56 5.102313 GGGTGGCTTTGAATTATTTCTTCG 58.898 41.667 0.00 0.00 32.78 3.79
66 67 1.460255 CCCTCTGGGTGGCTTTGAA 59.540 57.895 0.00 0.00 38.25 2.69
81 82 0.912006 GCCTGTTCTTCCTCTCCCCT 60.912 60.000 0.00 0.00 0.00 4.79
84 85 1.219393 CGGCCTGTTCTTCCTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
85 86 0.174617 CTCGGCCTGTTCTTCCTCTC 59.825 60.000 0.00 0.00 0.00 3.20
86 87 1.261238 CCTCGGCCTGTTCTTCCTCT 61.261 60.000 0.00 0.00 0.00 3.69
102 105 3.002371 CAGCCCTTCTTCCCCCTC 58.998 66.667 0.00 0.00 0.00 4.30
134 137 2.423898 TTGAGACCCGGAGATCGCC 61.424 63.158 0.73 5.23 37.59 5.54
147 150 3.706373 GAGCGGCCAGGGTTGAGA 61.706 66.667 2.24 0.00 0.00 3.27
167 170 0.976073 CTAAGAAGGAGGTGGGCCGA 60.976 60.000 0.00 0.00 40.50 5.54
171 174 1.763545 GTAGGCTAAGAAGGAGGTGGG 59.236 57.143 0.00 0.00 0.00 4.61
184 187 1.406903 GGGCGTAGAAAGGTAGGCTA 58.593 55.000 0.00 0.00 34.80 3.93
209 212 3.618780 GAGGCAGCCACAGGTCCTG 62.619 68.421 17.88 17.88 37.52 3.86
213 216 4.320456 CACGAGGCAGCCACAGGT 62.320 66.667 15.80 2.28 0.00 4.00
240 243 4.683334 GCTTTGTCCGCACGTGGC 62.683 66.667 18.88 8.78 39.90 5.01
252 255 2.427410 GTCGCGTTGGCTGCTTTG 60.427 61.111 5.77 0.00 36.88 2.77
253 256 2.591715 AGTCGCGTTGGCTGCTTT 60.592 55.556 5.77 0.00 36.88 3.51
254 257 3.044305 GAGTCGCGTTGGCTGCTT 61.044 61.111 5.77 0.00 36.88 3.91
317 320 2.514824 GCTCCGCCTGGAATCACC 60.515 66.667 0.00 0.00 45.87 4.02
318 321 2.514824 GGCTCCGCCTGGAATCAC 60.515 66.667 0.00 0.00 45.87 3.06
386 389 1.743995 GTAATGGAGTTGCCGCCGT 60.744 57.895 0.00 0.00 40.66 5.68
394 397 5.727434 ACGTTAAATCTCGGTAATGGAGTT 58.273 37.500 0.00 0.00 33.26 3.01
402 405 4.802039 GCAATCTGACGTTAAATCTCGGTA 59.198 41.667 0.00 0.00 0.00 4.02
403 406 3.617263 GCAATCTGACGTTAAATCTCGGT 59.383 43.478 0.00 0.00 0.00 4.69
404 407 3.865745 AGCAATCTGACGTTAAATCTCGG 59.134 43.478 0.00 0.00 0.00 4.63
440 445 0.037160 GGAAAGCAACCGACCCCTTA 59.963 55.000 0.00 0.00 0.00 2.69
441 446 1.228459 GGAAAGCAACCGACCCCTT 60.228 57.895 0.00 0.00 0.00 3.95
445 450 0.741915 TGTTTGGAAAGCAACCGACC 59.258 50.000 0.00 0.00 32.77 4.79
446 451 2.034053 TCATGTTTGGAAAGCAACCGAC 59.966 45.455 0.00 0.00 41.43 4.79
447 452 2.302260 TCATGTTTGGAAAGCAACCGA 58.698 42.857 0.00 0.00 41.43 4.69
448 453 2.791383 TCATGTTTGGAAAGCAACCG 57.209 45.000 0.00 0.00 41.43 4.44
458 463 3.196039 TGGATCCTTGCAATCATGTTTGG 59.804 43.478 14.23 0.00 0.00 3.28
459 464 4.459390 TGGATCCTTGCAATCATGTTTG 57.541 40.909 14.23 11.45 0.00 2.93
463 468 3.807622 GCAATTGGATCCTTGCAATCATG 59.192 43.478 25.99 10.44 42.37 3.07
474 479 9.396938 CAAACATTTTAAAAAGCAATTGGATCC 57.603 29.630 4.20 4.20 0.00 3.36
482 487 8.884726 GGTCCTTACAAACATTTTAAAAAGCAA 58.115 29.630 4.44 0.00 0.00 3.91
484 489 8.547894 CAGGTCCTTACAAACATTTTAAAAAGC 58.452 33.333 4.44 0.00 0.00 3.51
551 557 4.101585 TGTCAGTGTCTCTTCCACAGATTT 59.898 41.667 0.00 0.00 35.24 2.17
552 558 3.643320 TGTCAGTGTCTCTTCCACAGATT 59.357 43.478 0.00 0.00 35.24 2.40
553 559 3.234353 TGTCAGTGTCTCTTCCACAGAT 58.766 45.455 0.00 0.00 35.24 2.90
589 595 7.505585 AGAATTGATTGTTTGAGGGTTAACTGA 59.494 33.333 5.42 0.00 0.00 3.41
597 603 7.452880 TGTAAGAGAATTGATTGTTTGAGGG 57.547 36.000 0.00 0.00 0.00 4.30
598 604 7.487189 GCATGTAAGAGAATTGATTGTTTGAGG 59.513 37.037 0.00 0.00 0.00 3.86
611 617 1.565759 TGGGGCTGCATGTAAGAGAAT 59.434 47.619 0.50 0.00 0.00 2.40
621 627 3.380471 TTATAACAACTGGGGCTGCAT 57.620 42.857 0.50 0.00 0.00 3.96
625 631 4.584638 TGTGATTATAACAACTGGGGCT 57.415 40.909 0.00 0.00 0.00 5.19
646 653 7.849804 ATAGTCGAGTGCTTTACAATTGATT 57.150 32.000 13.59 0.00 38.92 2.57
681 688 0.901827 TATCGAGGCCAGCTGTTTCA 59.098 50.000 13.81 0.00 0.00 2.69
685 692 1.680522 CCAGTATCGAGGCCAGCTGT 61.681 60.000 13.81 0.00 0.00 4.40
690 697 0.554305 TCCTACCAGTATCGAGGCCA 59.446 55.000 5.01 0.00 0.00 5.36
692 699 1.340568 GGTTCCTACCAGTATCGAGGC 59.659 57.143 0.00 0.00 44.36 4.70
702 709 2.612746 GGGCCAGGGTTCCTACCA 60.613 66.667 4.39 0.00 46.96 3.25
703 710 3.793888 CGGGCCAGGGTTCCTACC 61.794 72.222 4.39 0.00 44.22 3.18
708 715 0.034863 TACAATTCGGGCCAGGGTTC 60.035 55.000 4.39 0.00 0.00 3.62
709 716 0.406361 TTACAATTCGGGCCAGGGTT 59.594 50.000 4.39 0.00 0.00 4.11
739 785 6.017770 CCCACAACAGTTCGTGAAGTAAATAA 60.018 38.462 14.10 0.00 35.02 1.40
758 804 5.593285 AACTTCTCAAAGTGCAACCCACAA 61.593 41.667 0.00 0.00 45.07 3.33
763 809 4.142381 ACTTCAACTTCTCAAAGTGCAACC 60.142 41.667 0.00 0.00 45.07 3.77
800 846 8.260818 AGAATTCTCCGAGTTGATTCTTGATTA 58.739 33.333 0.88 0.00 0.00 1.75
801 847 7.108847 AGAATTCTCCGAGTTGATTCTTGATT 58.891 34.615 0.88 0.00 0.00 2.57
802 848 6.648192 AGAATTCTCCGAGTTGATTCTTGAT 58.352 36.000 0.88 0.72 0.00 2.57
803 849 6.042638 AGAATTCTCCGAGTTGATTCTTGA 57.957 37.500 0.88 0.00 0.00 3.02
804 850 6.734104 AAGAATTCTCCGAGTTGATTCTTG 57.266 37.500 22.13 0.00 36.09 3.02
805 851 6.091441 CGAAAGAATTCTCCGAGTTGATTCTT 59.909 38.462 19.44 19.72 38.17 2.52
817 863 6.725246 TCACAAAGAAACGAAAGAATTCTCC 58.275 36.000 8.78 3.18 38.91 3.71
858 904 5.511234 AGCAGTACCGTATCGAGTTAATT 57.489 39.130 0.00 0.00 0.00 1.40
976 1022 1.153229 GGGTACGGTGGAAGGATGC 60.153 63.158 0.00 0.00 0.00 3.91
1038 1084 2.037251 AGTGAACAATAGCGTGTGGAGT 59.963 45.455 0.00 0.00 0.00 3.85
1049 1095 6.183360 TGCTCTATGGATCGAAGTGAACAATA 60.183 38.462 0.00 0.00 0.00 1.90
1163 1215 3.063197 GCGAGGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
1164 1216 2.520741 GCGAGGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
1165 1217 1.152567 ATGCGAGGAGGAGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
1166 1218 1.152652 GATGCGAGGAGGAGGAGGA 60.153 63.158 0.00 0.00 0.00 3.71
1167 1219 2.206536 GGATGCGAGGAGGAGGAGG 61.207 68.421 0.00 0.00 0.00 4.30
1168 1220 1.456518 TGGATGCGAGGAGGAGGAG 60.457 63.158 0.00 0.00 0.00 3.69
1169 1221 1.758514 GTGGATGCGAGGAGGAGGA 60.759 63.158 0.00 0.00 0.00 3.71
1170 1222 1.743321 GAGTGGATGCGAGGAGGAGG 61.743 65.000 0.00 0.00 0.00 4.30
1171 1223 1.739049 GAGTGGATGCGAGGAGGAG 59.261 63.158 0.00 0.00 0.00 3.69
1214 1277 2.035469 TACCGGTCGTGGTAGCCA 59.965 61.111 12.40 0.00 43.56 4.75
1550 1622 1.585521 GTCACGACCGGCTATCACG 60.586 63.158 0.00 0.45 0.00 4.35
1588 1660 6.380079 ACAGACCCTGAATTATTCTCAGTT 57.620 37.500 6.50 0.00 38.96 3.16
1606 1678 6.246420 ACAGAAATATCAGTGCAAACAGAC 57.754 37.500 0.00 0.00 0.00 3.51
1646 2021 7.165154 TGCGTCTTTTCTTCGAAAATGTAAAAG 59.835 33.333 15.79 15.79 36.00 2.27
1680 2055 0.326264 ATGGCCGGCTTCATATCCTC 59.674 55.000 28.56 5.64 0.00 3.71
1720 2189 8.055181 TGGCTCTCAAAGGAATAAAATACAGAT 58.945 33.333 0.00 0.00 0.00 2.90
1817 2286 2.093869 CCAATTGGCAGGTCATTCCAAG 60.094 50.000 12.53 0.00 42.43 3.61
1828 2297 9.767228 TGAAATTCATAATAATCCAATTGGCAG 57.233 29.630 20.33 0.00 34.44 4.85
1853 2322 6.969366 TCCTGTGATACAATCAAACAAACTG 58.031 36.000 0.00 0.00 41.69 3.16
1903 2381 5.500234 TGGGAATTCTTGTATTCACTCCAG 58.500 41.667 5.23 0.00 38.48 3.86
1914 2392 6.423776 ACAACATTTCATGGGAATTCTTGT 57.576 33.333 5.23 1.31 31.93 3.16
1918 2396 9.434420 TCATTTTACAACATTTCATGGGAATTC 57.566 29.630 0.00 0.00 31.93 2.17
1974 2453 2.019249 TGGTCGTTCGATTCGTAGGAT 58.981 47.619 10.50 0.00 0.00 3.24
1996 2475 6.578023 AGAATCCTTGAGAATCTTTCCTACG 58.422 40.000 0.00 0.00 29.96 3.51
2085 2564 1.446792 ATGAGCTGGTTCTGTCGCG 60.447 57.895 0.00 0.00 0.00 5.87
2125 2604 9.965902 CTAATTATAATCTATTTGCCCTGGAGT 57.034 33.333 0.00 0.00 0.00 3.85
2126 2605 9.965902 ACTAATTATAATCTATTTGCCCTGGAG 57.034 33.333 0.00 0.00 0.00 3.86
2623 3105 1.272147 ACTCCCAAGCTTCATGGAACC 60.272 52.381 4.39 0.00 40.56 3.62
2625 3107 3.587061 TCTTACTCCCAAGCTTCATGGAA 59.413 43.478 4.39 0.00 40.56 3.53
2645 3127 3.200825 AGGGTCAATCGGTGATGATTTCT 59.799 43.478 0.00 0.00 38.90 2.52
2646 3128 3.545703 AGGGTCAATCGGTGATGATTTC 58.454 45.455 0.00 0.00 38.90 2.17
2652 3134 5.825593 ACATATAAGGGTCAATCGGTGAT 57.174 39.130 0.00 0.00 38.90 3.06
2734 3218 3.192844 CGGTCGGTGGCAAGTATATATCT 59.807 47.826 0.00 0.00 0.00 1.98
2735 3219 3.192001 TCGGTCGGTGGCAAGTATATATC 59.808 47.826 0.00 0.00 0.00 1.63
2736 3220 3.057033 GTCGGTCGGTGGCAAGTATATAT 60.057 47.826 0.00 0.00 0.00 0.86
2737 3221 2.294233 GTCGGTCGGTGGCAAGTATATA 59.706 50.000 0.00 0.00 0.00 0.86
2750 3234 2.030540 TGTACTTTTCTCTGTCGGTCGG 60.031 50.000 0.00 0.00 0.00 4.79
2805 3289 5.509501 CCATCGCCAAGCATATAATTTTGGT 60.510 40.000 6.27 0.00 41.62 3.67
2812 3296 4.887071 AGTTTTCCATCGCCAAGCATATAA 59.113 37.500 0.00 0.00 0.00 0.98
2820 4827 4.920640 TTTACAAGTTTTCCATCGCCAA 57.079 36.364 0.00 0.00 0.00 4.52
2821 4828 4.920640 TTTTACAAGTTTTCCATCGCCA 57.079 36.364 0.00 0.00 0.00 5.69
2823 4830 8.682128 TTGATATTTTACAAGTTTTCCATCGC 57.318 30.769 0.00 0.00 0.00 4.58
2921 4945 8.557592 TGTGCCATTTAAATGAATTGCAAATA 57.442 26.923 26.32 14.35 38.77 1.40
2963 4987 3.202906 AGAAGAACAAGCAAGCACGTAA 58.797 40.909 0.00 0.00 0.00 3.18
2965 4989 1.599542 GAGAAGAACAAGCAAGCACGT 59.400 47.619 0.00 0.00 0.00 4.49
2966 4990 1.599071 TGAGAAGAACAAGCAAGCACG 59.401 47.619 0.00 0.00 0.00 5.34
2967 4991 3.911661 ATGAGAAGAACAAGCAAGCAC 57.088 42.857 0.00 0.00 0.00 4.40
2968 4992 4.924305 AAATGAGAAGAACAAGCAAGCA 57.076 36.364 0.00 0.00 0.00 3.91
2969 4993 5.108103 CGAAAAATGAGAAGAACAAGCAAGC 60.108 40.000 0.00 0.00 0.00 4.01
2970 4994 5.108103 GCGAAAAATGAGAAGAACAAGCAAG 60.108 40.000 0.00 0.00 0.00 4.01
2971 4995 4.739716 GCGAAAAATGAGAAGAACAAGCAA 59.260 37.500 0.00 0.00 0.00 3.91
2972 4996 4.036734 AGCGAAAAATGAGAAGAACAAGCA 59.963 37.500 0.00 0.00 0.00 3.91
2973 4997 4.540824 AGCGAAAAATGAGAAGAACAAGC 58.459 39.130 0.00 0.00 0.00 4.01
2992 5016 9.191995 GGTTTAATCAAATTTCCCATATTAGCG 57.808 33.333 0.00 0.00 0.00 4.26
3001 5025 7.809546 TGGTTTTGGTTTAATCAAATTTCCC 57.190 32.000 4.11 3.88 34.58 3.97
3034 5060 8.093927 TGTTTTCTTTTCTTTTCAGGACATTGT 58.906 29.630 0.00 0.00 0.00 2.71
3043 5069 9.567848 GTGACATAGTGTTTTCTTTTCTTTTCA 57.432 29.630 0.00 0.00 0.00 2.69
3106 5132 9.796120 CATGTTAACACCGACCATTAAAAATAT 57.204 29.630 11.22 0.00 0.00 1.28
3114 5140 8.740123 TTTATATCATGTTAACACCGACCATT 57.260 30.769 11.22 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.