Multiple sequence alignment - TraesCS6A01G133900

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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 TraesCS6A01G133900 chr6A 100.000 3248 0 0 1 3248 106081778 106078531 0.000000e+00 5999.0
1 TraesCS6A01G133900 chr6A 84.962 133 14 5 324 451 71652676 71652807 2.630000e-26 130.0
2 TraesCS6A01G133900 chr6A 85.393 89 4 1 2858 2946 616825964 616825885 2.080000e-12 84.2
3 TraesCS6A01G133900 chr6D 91.072 2677 144 44 102 2736 88104649 88102026 0.000000e+00 3531.0
4 TraesCS6A01G133900 chr6D 85.194 439 17 13 2818 3248 88101841 88101443 1.080000e-109 407.0
5 TraesCS6A01G133900 chr6D 91.549 71 5 1 2735 2805 88101995 88101926 2.670000e-16 97.1
6 TraesCS6A01G133900 chr6B 94.158 1917 70 18 826 2736 166623392 166621512 0.000000e+00 2881.0
7 TraesCS6A01G133900 chr6B 82.692 312 21 10 2818 3123 166621323 166621039 2.500000e-61 246.0
8 TraesCS6A01G133900 chr6B 88.785 107 12 0 3142 3248 716945207 716945101 7.310000e-27 132.0
9 TraesCS6A01G133900 chr6B 98.113 53 1 0 2736 2788 166621480 166621428 3.450000e-15 93.5
10 TraesCS6A01G133900 chr7B 80.000 270 48 6 201 466 562095457 562095190 9.190000e-46 195.0
11 TraesCS6A01G133900 chr7B 77.928 222 44 5 214 433 94609253 94609471 2.030000e-27 134.0
12 TraesCS6A01G133900 chr7B 88.785 107 12 0 3142 3248 112591901 112591795 7.310000e-27 132.0
13 TraesCS6A01G133900 chr4B 86.364 176 20 3 3073 3248 410811155 410811326 4.280000e-44 189.0
14 TraesCS6A01G133900 chr4B 88.750 80 6 1 2911 2987 410811027 410811106 9.590000e-16 95.3
15 TraesCS6A01G133900 chr3A 80.237 253 47 2 210 460 453671035 453670784 1.540000e-43 187.0
16 TraesCS6A01G133900 chr3A 85.393 89 4 1 2858 2946 739548509 739548430 2.080000e-12 84.2
17 TraesCS6A01G133900 chr5D 83.756 197 31 1 241 437 93071433 93071238 5.530000e-43 185.0
18 TraesCS6A01G133900 chr5D 83.099 142 20 3 322 460 330312224 330312084 3.400000e-25 126.0
19 TraesCS6A01G133900 chr5A 80.000 225 33 9 238 460 665762780 665762994 4.340000e-34 156.0
20 TraesCS6A01G133900 chr2B 84.173 139 20 2 324 460 747809196 747809058 2.030000e-27 134.0
21 TraesCS6A01G133900 chr7A 75.875 257 56 6 208 460 344677286 344677540 3.400000e-25 126.0
22 TraesCS6A01G133900 chr7A 75.620 242 52 6 223 460 85218910 85219148 2.650000e-21 113.0
23 TraesCS6A01G133900 chr7A 85.393 89 4 1 2858 2946 103126663 103126584 2.080000e-12 84.2
24 TraesCS6A01G133900 chr1D 77.157 197 41 4 208 403 220406489 220406682 9.530000e-21 111.0
25 TraesCS6A01G133900 chr2D 76.056 213 40 10 254 460 361260535 361260742 2.060000e-17 100.0
26 TraesCS6A01G133900 chrUn 85.393 89 4 1 2858 2946 341586027 341585948 2.080000e-12 84.2
27 TraesCS6A01G133900 chrUn 85.393 89 4 1 2858 2946 453615321 453615400 2.080000e-12 84.2
28 TraesCS6A01G133900 chr4A 85.393 89 4 1 2858 2946 714759915 714759836 2.080000e-12 84.2
29 TraesCS6A01G133900 chr1B 85.393 89 4 1 2858 2946 373693381 373693460 2.080000e-12 84.2
30 TraesCS6A01G133900 chr1B 100.000 28 0 0 1928 1955 456712056 456712029 6.000000e-03 52.8
31 TraesCS6A01G133900 chr1A 85.393 89 4 1 2858 2946 574280301 574280222 2.080000e-12 84.2
32 TraesCS6A01G133900 chr1A 85.542 83 3 1 2864 2946 592564354 592564281 9.660000e-11 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 TraesCS6A01G133900 chr6A 106078531 106081778 3247 True 5999.000000 5999 100.000000 1 3248 1 chr6A.!!$R1 3247
1 TraesCS6A01G133900 chr6D 88101443 88104649 3206 True 1345.033333 3531 89.271667 102 3248 3 chr6D.!!$R1 3146
2 TraesCS6A01G133900 chr6B 166621039 166623392 2353 True 1073.500000 2881 91.654333 826 3123 3 chr6B.!!$R2 2297

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
799 835 0.175989 GAAGGTAAGCGGGACTCCAG 59.824 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2592 2650 1.041437 CTCCAGTCCCCCTATTCGTC 58.959 60.0 0.0 0.0 0.0 4.2 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
18 19 3.608760 TGGTTCACCGCGTATTGAA 57.391 47.368 4.92 8.17 39.43 2.69
19 20 1.880271 TGGTTCACCGCGTATTGAAA 58.120 45.000 14.40 1.02 39.43 2.69
20 21 2.428491 TGGTTCACCGCGTATTGAAAT 58.572 42.857 14.40 0.00 39.43 2.17
21 22 3.597255 TGGTTCACCGCGTATTGAAATA 58.403 40.909 14.40 6.28 39.43 1.40
22 23 4.001652 TGGTTCACCGCGTATTGAAATAA 58.998 39.130 14.40 3.76 39.43 1.40
23 24 4.636648 TGGTTCACCGCGTATTGAAATAAT 59.363 37.500 14.40 0.00 39.43 1.28
24 25 5.816258 TGGTTCACCGCGTATTGAAATAATA 59.184 36.000 14.40 1.12 39.43 0.98
25 26 6.483974 TGGTTCACCGCGTATTGAAATAATAT 59.516 34.615 14.40 0.00 39.43 1.28
26 27 7.656542 TGGTTCACCGCGTATTGAAATAATATA 59.343 33.333 14.40 0.00 39.43 0.86
27 28 7.953710 GGTTCACCGCGTATTGAAATAATATAC 59.046 37.037 14.40 3.50 33.58 1.47
28 29 7.585286 TCACCGCGTATTGAAATAATATACC 57.415 36.000 4.92 0.00 0.00 2.73
29 30 6.591062 TCACCGCGTATTGAAATAATATACCC 59.409 38.462 4.92 0.00 0.00 3.69
30 31 5.876460 ACCGCGTATTGAAATAATATACCCC 59.124 40.000 4.92 0.00 0.00 4.95
31 32 5.875910 CCGCGTATTGAAATAATATACCCCA 59.124 40.000 4.92 0.00 0.00 4.96
32 33 6.540914 CCGCGTATTGAAATAATATACCCCAT 59.459 38.462 4.92 0.00 0.00 4.00
33 34 7.066525 CCGCGTATTGAAATAATATACCCCATT 59.933 37.037 4.92 0.00 0.00 3.16
34 35 9.100554 CGCGTATTGAAATAATATACCCCATTA 57.899 33.333 0.00 0.00 0.00 1.90
71 72 9.967451 TTCAATGGGTACTAAAAGTATTCATCA 57.033 29.630 0.00 0.00 32.65 3.07
74 75 9.920946 AATGGGTACTAAAAGTATTCATCATGT 57.079 29.630 0.00 0.00 32.65 3.21
139 141 9.889128 ATTTAAATGCATGGCAAGTACTATTTT 57.111 25.926 0.00 0.00 43.62 1.82
146 148 7.596995 TGCATGGCAAGTACTATTTTAAAACAC 59.403 33.333 1.97 0.00 34.76 3.32
147 149 7.596995 GCATGGCAAGTACTATTTTAAAACACA 59.403 33.333 1.97 0.00 0.00 3.72
148 150 9.469807 CATGGCAAGTACTATTTTAAAACACAA 57.530 29.630 1.97 0.00 0.00 3.33
228 234 7.173863 ATACTACTTGTAAATGCATACGTGC 57.826 36.000 0.00 0.00 42.10 5.34
241 247 4.630894 CATACGTGCAACCCACATTAAT 57.369 40.909 0.00 0.00 44.91 1.40
242 248 5.743026 CATACGTGCAACCCACATTAATA 57.257 39.130 0.00 0.00 44.91 0.98
243 249 6.312399 CATACGTGCAACCCACATTAATAT 57.688 37.500 0.00 0.00 44.91 1.28
245 251 5.652994 ACGTGCAACCCACATTAATATTT 57.347 34.783 0.00 0.00 44.91 1.40
247 253 6.791303 ACGTGCAACCCACATTAATATTTAG 58.209 36.000 0.00 0.00 44.91 1.85
248 254 6.183360 ACGTGCAACCCACATTAATATTTAGG 60.183 38.462 0.00 0.00 44.91 2.69
250 256 7.425606 GTGCAACCCACATTAATATTTAGGAG 58.574 38.462 0.00 0.00 44.06 3.69
330 356 9.063615 TGAATAGTAGTAGACGCTGATATTTGA 57.936 33.333 0.00 0.00 0.00 2.69
367 394 2.619013 GCTAAACATGTTGAGCGCTT 57.381 45.000 28.15 7.02 37.32 4.68
374 401 2.427410 GTTGAGCGCTTGCCGTTG 60.427 61.111 13.26 0.00 40.41 4.10
375 402 2.590291 TTGAGCGCTTGCCGTTGA 60.590 55.556 13.26 0.00 40.41 3.18
388 415 5.637006 TTGCCGTTGAAGCAATATAAGTT 57.363 34.783 0.00 0.00 44.95 2.66
398 425 8.347004 TGAAGCAATATAAGTTGTTGGATTGA 57.653 30.769 0.00 0.00 0.00 2.57
407 434 4.947645 AGTTGTTGGATTGACATGGTTTG 58.052 39.130 0.00 0.00 0.00 2.93
409 436 4.582701 TGTTGGATTGACATGGTTTGAC 57.417 40.909 0.00 0.00 0.00 3.18
643 679 8.971073 CCCAGAGAAGAAATTAAACCACATAAT 58.029 33.333 0.00 0.00 0.00 1.28
671 707 5.878669 CCTACAATACTAAGGAAAAACCGCT 59.121 40.000 0.00 0.00 44.74 5.52
686 722 2.898705 ACCGCTGCAAAAACAAAATGA 58.101 38.095 0.00 0.00 0.00 2.57
694 730 7.096106 CGCTGCAAAAACAAAATGATAAGAGAA 60.096 33.333 0.00 0.00 0.00 2.87
713 749 6.459923 AGAGAACCACAGAAAACTCATCTAC 58.540 40.000 0.00 0.00 0.00 2.59
721 757 6.036517 CACAGAAAACTCATCTACTACATGCC 59.963 42.308 0.00 0.00 0.00 4.40
722 758 6.108687 CAGAAAACTCATCTACTACATGCCA 58.891 40.000 0.00 0.00 0.00 4.92
725 761 7.665559 AGAAAACTCATCTACTACATGCCAAAA 59.334 33.333 0.00 0.00 0.00 2.44
726 762 7.759489 AAACTCATCTACTACATGCCAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
747 783 1.995376 AAAAGAACATTCGGGTGCCT 58.005 45.000 0.00 0.00 0.00 4.75
782 818 2.046700 GCCGACCCATCAACCGAA 60.047 61.111 0.00 0.00 0.00 4.30
783 819 2.106683 GCCGACCCATCAACCGAAG 61.107 63.158 0.00 0.00 0.00 3.79
796 832 4.808649 CGAAGGTAAGCGGGACTC 57.191 61.111 0.00 0.00 0.00 3.36
797 833 1.141234 CGAAGGTAAGCGGGACTCC 59.859 63.158 0.00 0.00 0.00 3.85
798 834 1.601419 CGAAGGTAAGCGGGACTCCA 61.601 60.000 0.00 0.00 0.00 3.86
799 835 0.175989 GAAGGTAAGCGGGACTCCAG 59.824 60.000 0.00 0.00 0.00 3.86
800 836 1.900545 AAGGTAAGCGGGACTCCAGC 61.901 60.000 11.99 11.99 34.41 4.85
801 837 2.187163 GTAAGCGGGACTCCAGCC 59.813 66.667 15.83 0.00 34.63 4.85
802 838 2.284331 TAAGCGGGACTCCAGCCA 60.284 61.111 15.83 2.62 34.63 4.75
872 923 1.801395 GCTCATACAGACGCGCCTTTA 60.801 52.381 5.73 0.00 0.00 1.85
873 924 2.536365 CTCATACAGACGCGCCTTTAA 58.464 47.619 5.73 0.00 0.00 1.52
874 925 2.264813 TCATACAGACGCGCCTTTAAC 58.735 47.619 5.73 0.00 0.00 2.01
875 926 2.094390 TCATACAGACGCGCCTTTAACT 60.094 45.455 5.73 0.00 0.00 2.24
876 927 1.986698 TACAGACGCGCCTTTAACTC 58.013 50.000 5.73 0.00 0.00 3.01
877 928 0.317479 ACAGACGCGCCTTTAACTCT 59.683 50.000 5.73 0.00 0.00 3.24
878 929 1.542915 ACAGACGCGCCTTTAACTCTA 59.457 47.619 5.73 0.00 0.00 2.43
879 930 1.918609 CAGACGCGCCTTTAACTCTAC 59.081 52.381 5.73 0.00 0.00 2.59
885 936 3.242248 CGCGCCTTTAACTCTACATACAC 59.758 47.826 0.00 0.00 0.00 2.90
886 937 3.554731 GCGCCTTTAACTCTACATACACC 59.445 47.826 0.00 0.00 0.00 4.16
933 991 0.675633 CAGAACCCAACCCAAAGCAG 59.324 55.000 0.00 0.00 0.00 4.24
972 1030 3.425659 CTCAGAAGGGGAAAAGAAAGGG 58.574 50.000 0.00 0.00 0.00 3.95
974 1032 3.465588 TCAGAAGGGGAAAAGAAAGGGAA 59.534 43.478 0.00 0.00 0.00 3.97
976 1034 4.653801 CAGAAGGGGAAAAGAAAGGGAAAA 59.346 41.667 0.00 0.00 0.00 2.29
977 1035 5.130311 CAGAAGGGGAAAAGAAAGGGAAAAA 59.870 40.000 0.00 0.00 0.00 1.94
1653 1711 1.324383 TCGTCTTCACACAGGCAGTA 58.676 50.000 0.00 0.00 0.00 2.74
1785 1843 2.374342 CTGGAGGTGGGGGAGGAT 59.626 66.667 0.00 0.00 0.00 3.24
1932 1990 1.004745 GAGGTGATTGCAGGAGGGAAA 59.995 52.381 0.00 0.00 0.00 3.13
2040 2098 4.627284 TGAAAACCGTGGAATTCCTCTA 57.373 40.909 24.73 2.19 36.82 2.43
2391 2449 1.709578 TTACCATTGCACAAAGGGCA 58.290 45.000 9.27 0.00 43.86 5.36
2429 2487 6.695429 TGATGCTGAATCTGGTCATATACTC 58.305 40.000 0.00 0.00 36.15 2.59
2430 2488 5.126396 TGCTGAATCTGGTCATATACTCG 57.874 43.478 0.00 0.00 0.00 4.18
2437 2495 8.204160 TGAATCTGGTCATATACTCGTTGAAAT 58.796 33.333 0.00 0.00 0.00 2.17
2533 2591 4.006780 AGGGACAAACATTGATTTTGCC 57.993 40.909 0.00 0.00 37.45 4.52
2535 2593 4.041938 AGGGACAAACATTGATTTTGCCAT 59.958 37.500 6.22 2.14 37.45 4.40
2552 2610 2.420547 GCCATGCCAGTTCACTCAGATA 60.421 50.000 0.00 0.00 0.00 1.98
2558 2616 4.081642 TGCCAGTTCACTCAGATAGTAACC 60.082 45.833 0.00 0.00 35.76 2.85
2559 2617 4.081642 GCCAGTTCACTCAGATAGTAACCA 60.082 45.833 0.00 0.00 35.76 3.67
2560 2618 5.568825 GCCAGTTCACTCAGATAGTAACCAA 60.569 44.000 0.00 0.00 35.76 3.67
2585 2643 5.238432 CACTGAGATAGTTCGCTGAGATAGT 59.762 44.000 0.00 0.00 37.60 2.12
2592 2650 5.000012 AGTTCGCTGAGATAGTAACCAAG 58.000 43.478 0.00 0.00 0.00 3.61
2595 2653 3.064958 TCGCTGAGATAGTAACCAAGACG 59.935 47.826 0.00 0.00 0.00 4.18
2606 2664 1.201424 ACCAAGACGAATAGGGGGAC 58.799 55.000 0.00 0.00 0.00 4.46
2610 2668 0.635009 AGACGAATAGGGGGACTGGA 59.365 55.000 0.00 0.00 0.00 3.86
2650 2709 8.443953 TTTCTTGTATGGTTTTGAAAATTGGG 57.556 30.769 0.00 0.00 0.00 4.12
2654 2714 3.205784 TGGTTTTGAAAATTGGGCTGG 57.794 42.857 0.00 0.00 0.00 4.85
2702 2765 9.686683 ATGTTTCTAAAAATAGTCTATGTGCCT 57.313 29.630 0.00 0.00 0.00 4.75
2715 2778 2.031919 TGCCTTCGGACAATGCGT 59.968 55.556 0.00 0.00 31.47 5.24
2774 2869 2.281276 GACCCAACCGACACACCC 60.281 66.667 0.00 0.00 0.00 4.61
2790 2893 3.055675 CACACCCGGAATACCTTTAGACA 60.056 47.826 0.73 0.00 0.00 3.41
2796 2899 5.296035 CCCGGAATACCTTTAGACACATTTC 59.704 44.000 0.73 0.00 0.00 2.17
2801 2904 7.606456 GGAATACCTTTAGACACATTTCACTCA 59.394 37.037 0.00 0.00 0.00 3.41
2802 2905 8.553459 AATACCTTTAGACACATTTCACTCAG 57.447 34.615 0.00 0.00 0.00 3.35
2807 2910 7.118390 CCTTTAGACACATTTCACTCAGTTAGG 59.882 40.741 0.00 0.00 0.00 2.69
2808 2911 5.808366 AGACACATTTCACTCAGTTAGGA 57.192 39.130 0.00 0.00 0.00 2.94
2809 2912 6.365970 AGACACATTTCACTCAGTTAGGAT 57.634 37.500 0.00 0.00 0.00 3.24
2812 2987 6.299141 ACACATTTCACTCAGTTAGGATGTT 58.701 36.000 0.00 0.00 0.00 2.71
2815 2990 7.387673 CACATTTCACTCAGTTAGGATGTTGTA 59.612 37.037 0.00 0.00 0.00 2.41
2816 2991 8.103305 ACATTTCACTCAGTTAGGATGTTGTAT 58.897 33.333 0.00 0.00 0.00 2.29
2830 3005 7.125391 AGGATGTTGTATGATACCCATGTTTT 58.875 34.615 8.89 0.00 36.71 2.43
2871 3047 7.673926 AGGGGTGACATATAATGTTGAAGTTTT 59.326 33.333 0.00 0.00 45.03 2.43
2942 3118 8.918202 TTGTGTTAAAATCAGAGGACTACAAT 57.082 30.769 0.00 0.00 0.00 2.71
2966 3148 0.328258 GTGGTGTGGGAGTGCCTTAT 59.672 55.000 1.06 0.00 0.00 1.73
2981 3163 4.338400 GTGCCTTATACCATTTTGAGTCCC 59.662 45.833 0.00 0.00 0.00 4.46
2987 3169 7.396055 CCTTATACCATTTTGAGTCCCTTTTGA 59.604 37.037 0.00 0.00 0.00 2.69
2990 3172 3.321682 CCATTTTGAGTCCCTTTTGAGCA 59.678 43.478 0.00 0.00 0.00 4.26
2991 3173 4.202243 CCATTTTGAGTCCCTTTTGAGCAA 60.202 41.667 0.00 0.00 0.00 3.91
2992 3174 4.654091 TTTTGAGTCCCTTTTGAGCAAG 57.346 40.909 0.00 0.00 0.00 4.01
2993 3175 2.276732 TGAGTCCCTTTTGAGCAAGG 57.723 50.000 0.00 0.00 42.91 3.61
3002 3184 4.318332 CCTTTTGAGCAAGGGATTTTTCC 58.682 43.478 0.00 0.00 39.95 3.13
3003 3185 4.202346 CCTTTTGAGCAAGGGATTTTTCCA 60.202 41.667 0.00 0.00 39.95 3.53
3004 3186 4.605640 TTTGAGCAAGGGATTTTTCCAG 57.394 40.909 0.00 0.00 0.00 3.86
3005 3187 3.524095 TGAGCAAGGGATTTTTCCAGA 57.476 42.857 0.00 0.00 0.00 3.86
3006 3188 3.843422 TGAGCAAGGGATTTTTCCAGAA 58.157 40.909 0.00 0.00 0.00 3.02
3007 3189 3.573967 TGAGCAAGGGATTTTTCCAGAAC 59.426 43.478 0.00 0.00 0.00 3.01
3008 3190 2.899900 AGCAAGGGATTTTTCCAGAACC 59.100 45.455 0.00 0.00 0.00 3.62
3009 3191 2.632512 GCAAGGGATTTTTCCAGAACCA 59.367 45.455 0.00 0.00 0.00 3.67
3015 3197 6.071320 AGGGATTTTTCCAGAACCATATAGC 58.929 40.000 0.00 0.00 0.00 2.97
3087 3271 5.046950 GTGAAGGTGATGTAGGGATCTATCC 60.047 48.000 0.00 0.00 46.41 2.59
3186 3370 0.634465 GGGAAAATGGGGCTAAGGGA 59.366 55.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.880271 TTTCAATACGCGGTGAACCA 58.120 45.000 18.04 5.89 33.58 3.67
1 2 4.603231 TTATTTCAATACGCGGTGAACC 57.397 40.909 18.04 0.00 33.58 3.62
2 3 7.953710 GGTATATTATTTCAATACGCGGTGAAC 59.046 37.037 18.04 7.98 33.58 3.18
3 4 7.118101 GGGTATATTATTTCAATACGCGGTGAA 59.882 37.037 12.47 14.32 31.92 3.18
4 5 6.591062 GGGTATATTATTTCAATACGCGGTGA 59.409 38.462 12.47 8.30 31.92 4.02
5 6 6.183360 GGGGTATATTATTTCAATACGCGGTG 60.183 42.308 12.47 5.63 38.95 4.94
6 7 5.876460 GGGGTATATTATTTCAATACGCGGT 59.124 40.000 12.47 0.00 38.95 5.68
7 8 5.875910 TGGGGTATATTATTTCAATACGCGG 59.124 40.000 12.47 0.00 38.95 6.46
8 9 6.971527 TGGGGTATATTATTTCAATACGCG 57.028 37.500 3.53 3.53 38.95 6.01
45 46 9.967451 TGATGAATACTTTTAGTACCCATTGAA 57.033 29.630 0.00 0.00 32.84 2.69
48 49 9.920946 ACATGATGAATACTTTTAGTACCCATT 57.079 29.630 0.00 0.00 32.84 3.16
120 121 7.596995 GTGTTTTAAAATAGTACTTGCCATGCA 59.403 33.333 0.00 0.00 36.47 3.96
121 122 7.596995 TGTGTTTTAAAATAGTACTTGCCATGC 59.403 33.333 0.00 0.00 0.00 4.06
221 227 6.952773 AATATTAATGTGGGTTGCACGTAT 57.047 33.333 0.00 0.00 0.00 3.06
222 228 6.761099 AAATATTAATGTGGGTTGCACGTA 57.239 33.333 0.00 0.00 0.00 3.57
223 229 5.652994 AAATATTAATGTGGGTTGCACGT 57.347 34.783 0.00 0.00 0.00 4.49
224 230 6.038825 TCCTAAATATTAATGTGGGTTGCACG 59.961 38.462 0.00 0.00 0.00 5.34
225 231 7.284489 TCTCCTAAATATTAATGTGGGTTGCAC 59.716 37.037 0.00 0.00 0.00 4.57
226 232 7.350382 TCTCCTAAATATTAATGTGGGTTGCA 58.650 34.615 0.00 0.00 0.00 4.08
227 233 7.817418 TCTCCTAAATATTAATGTGGGTTGC 57.183 36.000 0.00 0.00 0.00 4.17
301 327 6.885952 ATCAGCGTCTACTACTATTCATGT 57.114 37.500 0.00 0.00 0.00 3.21
347 373 1.522668 AGCGCTCAACATGTTTAGCA 58.477 45.000 32.86 9.93 39.16 3.49
348 374 2.245096 CAAGCGCTCAACATGTTTAGC 58.755 47.619 27.50 27.50 36.68 3.09
367 394 4.457603 ACAACTTATATTGCTTCAACGGCA 59.542 37.500 0.00 0.00 37.97 5.69
374 401 8.243426 TGTCAATCCAACAACTTATATTGCTTC 58.757 33.333 0.00 0.00 32.47 3.86
375 402 8.121305 TGTCAATCCAACAACTTATATTGCTT 57.879 30.769 0.00 0.00 32.47 3.91
385 412 4.648762 TCAAACCATGTCAATCCAACAACT 59.351 37.500 0.00 0.00 0.00 3.16
388 415 3.004210 CGTCAAACCATGTCAATCCAACA 59.996 43.478 0.00 0.00 0.00 3.33
398 425 1.671054 CTCGGCCGTCAAACCATGT 60.671 57.895 27.15 0.00 0.00 3.21
407 434 4.391140 GATTCAATAAATCTCGGCCGTC 57.609 45.455 27.15 6.40 40.62 4.79
460 490 8.447053 GTTCACTGGATGTTAAGAAAGATCTTC 58.553 37.037 8.78 2.74 44.75 2.87
565 595 8.231837 GCATTTCAAATTTGTTTCATAGTGCAT 58.768 29.630 17.47 0.00 0.00 3.96
566 596 7.226128 TGCATTTCAAATTTGTTTCATAGTGCA 59.774 29.630 17.47 17.46 33.55 4.57
567 597 7.574496 TGCATTTCAAATTTGTTTCATAGTGC 58.426 30.769 17.47 15.62 0.00 4.40
568 598 9.932699 TTTGCATTTCAAATTTGTTTCATAGTG 57.067 25.926 17.47 7.94 39.58 2.74
570 600 9.601971 CCTTTGCATTTCAAATTTGTTTCATAG 57.398 29.630 17.47 12.37 43.14 2.23
571 601 8.566260 CCCTTTGCATTTCAAATTTGTTTCATA 58.434 29.630 17.47 0.00 43.14 2.15
572 602 7.068470 ACCCTTTGCATTTCAAATTTGTTTCAT 59.932 29.630 17.47 3.72 43.14 2.57
573 603 6.376581 ACCCTTTGCATTTCAAATTTGTTTCA 59.623 30.769 17.47 7.46 43.14 2.69
574 604 6.692249 CACCCTTTGCATTTCAAATTTGTTTC 59.308 34.615 17.47 5.23 43.14 2.78
575 605 6.376581 TCACCCTTTGCATTTCAAATTTGTTT 59.623 30.769 17.47 1.76 43.14 2.83
576 606 5.884792 TCACCCTTTGCATTTCAAATTTGTT 59.115 32.000 17.47 2.11 43.14 2.83
577 607 5.296531 GTCACCCTTTGCATTTCAAATTTGT 59.703 36.000 17.47 0.00 43.14 2.83
617 653 6.840780 ATGTGGTTTAATTTCTTCTCTGGG 57.159 37.500 0.00 0.00 0.00 4.45
643 679 7.170277 GGTTTTTCCTTAGTATTGTAGGGTCA 58.830 38.462 0.00 0.00 0.00 4.02
666 702 2.898705 TCATTTTGTTTTTGCAGCGGT 58.101 38.095 0.00 0.00 0.00 5.68
671 707 7.984050 TGGTTCTCTTATCATTTTGTTTTTGCA 59.016 29.630 0.00 0.00 0.00 4.08
686 722 7.684529 AGATGAGTTTTCTGTGGTTCTCTTAT 58.315 34.615 0.00 0.00 0.00 1.73
694 730 6.665992 TGTAGTAGATGAGTTTTCTGTGGT 57.334 37.500 0.00 0.00 0.00 4.16
727 763 2.035832 CAGGCACCCGAATGTTCTTTTT 59.964 45.455 0.00 0.00 0.00 1.94
728 764 1.613437 CAGGCACCCGAATGTTCTTTT 59.387 47.619 0.00 0.00 0.00 2.27
729 765 1.247567 CAGGCACCCGAATGTTCTTT 58.752 50.000 0.00 0.00 0.00 2.52
730 766 1.244019 GCAGGCACCCGAATGTTCTT 61.244 55.000 0.00 0.00 0.00 2.52
731 767 1.675641 GCAGGCACCCGAATGTTCT 60.676 57.895 0.00 0.00 0.00 3.01
732 768 2.700773 GGCAGGCACCCGAATGTTC 61.701 63.158 0.00 0.00 0.00 3.18
733 769 2.676471 GGCAGGCACCCGAATGTT 60.676 61.111 0.00 0.00 0.00 2.71
734 770 3.965258 TGGCAGGCACCCGAATGT 61.965 61.111 0.00 0.00 0.00 2.71
735 771 3.443045 GTGGCAGGCACCCGAATG 61.443 66.667 16.38 0.00 0.00 2.67
782 818 2.359967 GCTGGAGTCCCGCTTACCT 61.360 63.158 17.63 0.00 34.29 3.08
783 819 2.187163 GCTGGAGTCCCGCTTACC 59.813 66.667 17.63 0.00 34.29 2.85
784 820 2.187163 GGCTGGAGTCCCGCTTAC 59.813 66.667 22.98 5.18 34.15 2.34
785 821 2.284331 TGGCTGGAGTCCCGCTTA 60.284 61.111 22.98 11.35 34.15 3.09
788 824 4.767255 CTGTGGCTGGAGTCCCGC 62.767 72.222 16.74 16.74 34.29 6.13
789 825 1.903877 ATTCTGTGGCTGGAGTCCCG 61.904 60.000 6.74 0.39 34.29 5.14
790 826 0.107459 GATTCTGTGGCTGGAGTCCC 60.107 60.000 6.74 0.00 0.00 4.46
791 827 0.460987 CGATTCTGTGGCTGGAGTCC 60.461 60.000 0.73 0.73 0.00 3.85
792 828 0.460987 CCGATTCTGTGGCTGGAGTC 60.461 60.000 0.00 0.00 0.00 3.36
793 829 0.904865 TCCGATTCTGTGGCTGGAGT 60.905 55.000 0.00 0.00 0.00 3.85
794 830 0.179089 CTCCGATTCTGTGGCTGGAG 60.179 60.000 0.00 0.00 37.29 3.86
795 831 0.614697 TCTCCGATTCTGTGGCTGGA 60.615 55.000 0.00 0.00 0.00 3.86
796 832 0.250234 TTCTCCGATTCTGTGGCTGG 59.750 55.000 0.00 0.00 0.00 4.85
797 833 2.005451 CTTTCTCCGATTCTGTGGCTG 58.995 52.381 0.00 0.00 0.00 4.85
798 834 1.902508 TCTTTCTCCGATTCTGTGGCT 59.097 47.619 0.00 0.00 0.00 4.75
799 835 2.275318 CTCTTTCTCCGATTCTGTGGC 58.725 52.381 0.00 0.00 0.00 5.01
800 836 2.275318 GCTCTTTCTCCGATTCTGTGG 58.725 52.381 0.00 0.00 0.00 4.17
801 837 2.275318 GGCTCTTTCTCCGATTCTGTG 58.725 52.381 0.00 0.00 0.00 3.66
802 838 1.208293 GGGCTCTTTCTCCGATTCTGT 59.792 52.381 0.00 0.00 0.00 3.41
872 923 2.570302 GGTGGTGGGTGTATGTAGAGTT 59.430 50.000 0.00 0.00 0.00 3.01
873 924 2.185387 GGTGGTGGGTGTATGTAGAGT 58.815 52.381 0.00 0.00 0.00 3.24
874 925 1.136305 CGGTGGTGGGTGTATGTAGAG 59.864 57.143 0.00 0.00 0.00 2.43
875 926 1.187974 CGGTGGTGGGTGTATGTAGA 58.812 55.000 0.00 0.00 0.00 2.59
876 927 0.461339 GCGGTGGTGGGTGTATGTAG 60.461 60.000 0.00 0.00 0.00 2.74
877 928 1.597989 GCGGTGGTGGGTGTATGTA 59.402 57.895 0.00 0.00 0.00 2.29
878 929 2.349755 GCGGTGGTGGGTGTATGT 59.650 61.111 0.00 0.00 0.00 2.29
879 930 2.437716 GGCGGTGGTGGGTGTATG 60.438 66.667 0.00 0.00 0.00 2.39
933 991 3.577313 GGAAGGAATCGCAGCGGC 61.577 66.667 16.42 0.00 0.00 6.53
977 1035 2.568090 CGGCTGCGGATGCTTTTT 59.432 55.556 0.00 0.00 43.34 1.94
978 1036 4.120331 GCGGCTGCGGATGCTTTT 62.120 61.111 11.68 0.00 43.34 2.27
1461 1519 4.570663 CCGTAGAGGAAGCCCGCG 62.571 72.222 0.00 0.00 45.00 6.46
1653 1711 4.722535 TCGCTGGCCTTCCTCCCT 62.723 66.667 3.32 0.00 0.00 4.20
2291 2349 5.363292 ACATGAGATGATACTGAGAGCAAGT 59.637 40.000 0.00 0.00 0.00 3.16
2391 2449 7.876068 AGATTCAGCATCAAAATGAAACATGTT 59.124 29.630 4.92 4.92 36.59 2.71
2429 2487 4.026640 CACCAAAAGACTTGCATTTCAACG 60.027 41.667 0.00 0.00 0.00 4.10
2430 2488 4.270808 CCACCAAAAGACTTGCATTTCAAC 59.729 41.667 0.00 0.00 0.00 3.18
2437 2495 2.175202 ACAACCACCAAAAGACTTGCA 58.825 42.857 0.00 0.00 0.00 4.08
2533 2591 4.134379 ACTATCTGAGTGAACTGGCATG 57.866 45.455 0.00 0.00 36.87 4.06
2535 2593 4.081642 GGTTACTATCTGAGTGAACTGGCA 60.082 45.833 0.00 0.00 39.39 4.92
2552 2610 5.710984 CGAACTATCTCAGTGTTGGTTACT 58.289 41.667 0.00 0.00 37.63 2.24
2558 2616 3.838120 TCAGCGAACTATCTCAGTGTTG 58.162 45.455 0.00 0.00 37.63 3.33
2559 2617 3.759086 TCTCAGCGAACTATCTCAGTGTT 59.241 43.478 0.00 0.00 37.63 3.32
2560 2618 3.348119 TCTCAGCGAACTATCTCAGTGT 58.652 45.455 0.00 0.00 37.63 3.55
2585 2643 2.767960 GTCCCCCTATTCGTCTTGGTTA 59.232 50.000 0.00 0.00 0.00 2.85
2592 2650 1.041437 CTCCAGTCCCCCTATTCGTC 58.959 60.000 0.00 0.00 0.00 4.20
2595 2653 2.050918 CCTTCTCCAGTCCCCCTATTC 58.949 57.143 0.00 0.00 0.00 1.75
2606 2664 5.259632 AGAAATTGATCAACCCTTCTCCAG 58.740 41.667 11.07 0.00 0.00 3.86
2610 2668 7.123247 CCATACAAGAAATTGATCAACCCTTCT 59.877 37.037 11.07 15.24 0.00 2.85
2646 2705 3.648067 CCTAAGTCATATCTCCAGCCCAA 59.352 47.826 0.00 0.00 0.00 4.12
2649 2708 3.243724 ACCCTAAGTCATATCTCCAGCC 58.756 50.000 0.00 0.00 0.00 4.85
2650 2709 4.529109 GACCCTAAGTCATATCTCCAGC 57.471 50.000 0.00 0.00 45.55 4.85
2702 2765 3.474904 CGCGACGCATTGTCCGAA 61.475 61.111 21.35 0.00 45.23 4.30
2715 2778 2.989253 TCTGACTTGCCCTCGCGA 60.989 61.111 9.26 9.26 38.08 5.87
2774 2869 6.594159 AGTGAAATGTGTCTAAAGGTATTCCG 59.406 38.462 0.00 0.00 39.05 4.30
2790 2893 6.299141 ACAACATCCTAACTGAGTGAAATGT 58.701 36.000 0.00 0.00 0.00 2.71
2796 2899 7.653713 GGTATCATACAACATCCTAACTGAGTG 59.346 40.741 0.00 0.00 0.00 3.51
2801 2904 7.072454 ACATGGGTATCATACAACATCCTAACT 59.928 37.037 0.00 0.00 34.12 2.24
2802 2905 7.224297 ACATGGGTATCATACAACATCCTAAC 58.776 38.462 0.00 0.00 34.12 2.34
2807 2910 7.706179 CCAAAAACATGGGTATCATACAACATC 59.294 37.037 0.00 0.00 36.79 3.06
2808 2911 7.180051 ACCAAAAACATGGGTATCATACAACAT 59.820 33.333 0.00 0.00 45.18 2.71
2809 2912 6.495181 ACCAAAAACATGGGTATCATACAACA 59.505 34.615 0.00 0.00 45.18 3.33
2812 2987 7.382110 CAAACCAAAAACATGGGTATCATACA 58.618 34.615 0.00 0.00 40.33 2.29
2815 2990 5.012975 AGCAAACCAAAAACATGGGTATCAT 59.987 36.000 0.00 0.00 40.33 2.45
2816 2991 4.346418 AGCAAACCAAAAACATGGGTATCA 59.654 37.500 0.00 0.00 40.33 2.15
2830 3005 0.178964 CCCCTCCTTGAGCAAACCAA 60.179 55.000 0.00 0.00 0.00 3.67
2871 3047 5.996644 TCAAAAACTCCAGACCTTACTTCA 58.003 37.500 0.00 0.00 0.00 3.02
2942 3118 1.477923 GGCACTCCCACACCACTTTTA 60.478 52.381 0.00 0.00 0.00 1.52
2966 3148 4.522789 GCTCAAAAGGGACTCAAAATGGTA 59.477 41.667 0.00 0.00 38.49 3.25
2981 3163 4.959723 TGGAAAAATCCCTTGCTCAAAAG 58.040 39.130 0.00 0.00 0.00 2.27
2987 3169 2.899900 GGTTCTGGAAAAATCCCTTGCT 59.100 45.455 0.00 0.00 0.00 3.91
2990 3172 6.551227 GCTATATGGTTCTGGAAAAATCCCTT 59.449 38.462 0.00 0.00 0.00 3.95
2991 3173 6.071320 GCTATATGGTTCTGGAAAAATCCCT 58.929 40.000 0.00 0.00 0.00 4.20
2992 3174 6.015940 CAGCTATATGGTTCTGGAAAAATCCC 60.016 42.308 0.00 0.00 0.00 3.85
2993 3175 6.547510 ACAGCTATATGGTTCTGGAAAAATCC 59.452 38.462 0.00 0.00 0.00 3.01
2994 3176 7.420800 CACAGCTATATGGTTCTGGAAAAATC 58.579 38.462 0.00 0.00 0.00 2.17
2995 3177 6.322201 CCACAGCTATATGGTTCTGGAAAAAT 59.678 38.462 3.20 0.00 0.00 1.82
2996 3178 5.652014 CCACAGCTATATGGTTCTGGAAAAA 59.348 40.000 3.20 0.00 0.00 1.94
2997 3179 5.045213 TCCACAGCTATATGGTTCTGGAAAA 60.045 40.000 9.92 0.00 37.27 2.29
2998 3180 4.473196 TCCACAGCTATATGGTTCTGGAAA 59.527 41.667 9.92 0.00 37.27 3.13
2999 3181 4.037222 TCCACAGCTATATGGTTCTGGAA 58.963 43.478 9.92 0.00 37.27 3.53
3000 3182 3.653164 TCCACAGCTATATGGTTCTGGA 58.347 45.455 9.92 0.00 37.27 3.86
3001 3183 4.573900 GATCCACAGCTATATGGTTCTGG 58.426 47.826 9.92 0.00 37.27 3.86
3002 3184 4.021981 TCGATCCACAGCTATATGGTTCTG 60.022 45.833 15.02 10.79 37.27 3.02
3003 3185 4.021894 GTCGATCCACAGCTATATGGTTCT 60.022 45.833 15.02 3.31 37.27 3.01
3004 3186 4.238514 GTCGATCCACAGCTATATGGTTC 58.761 47.826 9.92 10.01 37.27 3.62
3005 3187 3.641436 TGTCGATCCACAGCTATATGGTT 59.359 43.478 9.92 3.14 37.27 3.67
3006 3188 3.230976 TGTCGATCCACAGCTATATGGT 58.769 45.455 9.92 0.00 37.27 3.55
3007 3189 3.942130 TGTCGATCCACAGCTATATGG 57.058 47.619 4.75 4.75 37.32 2.74
3008 3190 4.021981 TCCTTGTCGATCCACAGCTATATG 60.022 45.833 0.00 0.00 0.00 1.78
3009 3191 4.152647 TCCTTGTCGATCCACAGCTATAT 58.847 43.478 0.00 0.00 0.00 0.86
3015 3197 5.376854 AAAAATTCCTTGTCGATCCACAG 57.623 39.130 0.00 0.00 0.00 3.66
3087 3271 3.146104 AGTCTCTCATGTGGGGTTTTG 57.854 47.619 0.00 0.00 0.00 2.44
3092 3276 3.813443 CCAAATAGTCTCTCATGTGGGG 58.187 50.000 0.00 0.00 0.00 4.96
3156 3340 3.069443 CCCCATTTTCCCATTTGTATCGG 59.931 47.826 0.00 0.00 0.00 4.18
3219 3403 7.066887 TGCTTGAAGTGTTTTCATCTCAAGTAA 59.933 33.333 10.37 0.00 44.30 2.24
3224 3408 5.125356 TCTGCTTGAAGTGTTTTCATCTCA 58.875 37.500 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.