Multiple sequence alignment - TraesCS5D01G057600

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 TraesCS5D01G057600 chr5D 100.000 2934 0 0 691 3624 54097284 54100217 0.000000e+00 5419
1 TraesCS5D01G057600 chr5D 100.000 410 0 0 1 410 54096594 54097003 0.000000e+00 758
2 TraesCS5D01G057600 chr5D 92.954 369 26 0 1801 2169 321998712 321999080 4.120000e-149 538
3 TraesCS5D01G057600 chr5B 91.558 2618 122 49 691 3257 56978880 56981449 0.000000e+00 3518
4 TraesCS5D01G057600 chr5B 94.189 912 39 6 979 1887 56915527 56916427 0.000000e+00 1378
5 TraesCS5D01G057600 chr5B 93.194 720 48 1 1454 2172 460971341 460970622 0.000000e+00 1057
6 TraesCS5D01G057600 chr5B 86.854 426 17 9 1 410 56978435 56978837 1.190000e-119 440
7 TraesCS5D01G057600 chr5B 88.997 309 19 7 691 990 56912735 56913037 5.720000e-98 368
8 TraesCS5D01G057600 chr5B 82.904 427 35 15 1 409 56695923 56696329 2.070000e-92 350
9 TraesCS5D01G057600 chr5B 88.542 288 17 8 691 969 56696343 56696623 5.800000e-88 335
10 TraesCS5D01G057600 chr5B 86.628 172 11 6 249 408 56912529 56912700 2.870000e-41 180
11 TraesCS5D01G057600 chr5B 97.753 89 2 0 2252 2340 460970539 460970451 1.740000e-33 154
12 TraesCS5D01G057600 chr5A 90.770 2611 132 44 691 3234 42259015 42261583 0.000000e+00 3386
13 TraesCS5D01G057600 chr5A 80.423 378 45 14 3254 3624 42261576 42261931 9.980000e-66 261
14 TraesCS5D01G057600 chr5A 82.596 339 15 13 16 341 42258589 42258896 3.590000e-65 259
15 TraesCS5D01G057600 chr7A 92.737 716 52 0 1454 2169 17262275 17262990 0.000000e+00 1035
16 TraesCS5D01G057600 chr3B 93.284 670 44 1 1503 2172 813200986 813200318 0.000000e+00 987
17 TraesCS5D01G057600 chr3B 95.506 89 4 0 2252 2340 813200233 813200145 3.770000e-30 143
18 TraesCS5D01G057600 chr2B 94.424 538 29 1 1455 1992 723045637 723046173 0.000000e+00 826
19 TraesCS5D01G057600 chr2B 93.530 541 33 2 1454 1992 785072155 785072695 0.000000e+00 804
20 TraesCS5D01G057600 chr7B 93.878 539 33 0 1454 1992 17357310 17356772 0.000000e+00 813


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 TraesCS5D01G057600 chr5D 54096594 54100217 3623 False 3088.5 5419 100.000000 1 3624 2 chr5D.!!$F2 3623
1 TraesCS5D01G057600 chr5B 56978435 56981449 3014 False 1979.0 3518 89.206000 1 3257 2 chr5B.!!$F3 3256
2 TraesCS5D01G057600 chr5B 56912529 56916427 3898 False 642.0 1378 89.938000 249 1887 3 chr5B.!!$F2 1638
3 TraesCS5D01G057600 chr5B 460970451 460971341 890 True 605.5 1057 95.473500 1454 2340 2 chr5B.!!$R1 886
4 TraesCS5D01G057600 chr5B 56695923 56696623 700 False 342.5 350 85.723000 1 969 2 chr5B.!!$F1 968
5 TraesCS5D01G057600 chr5A 42258589 42261931 3342 False 1302.0 3386 84.596333 16 3624 3 chr5A.!!$F1 3608
6 TraesCS5D01G057600 chr7A 17262275 17262990 715 False 1035.0 1035 92.737000 1454 2169 1 chr7A.!!$F1 715
7 TraesCS5D01G057600 chr3B 813200145 813200986 841 True 565.0 987 94.395000 1503 2340 2 chr3B.!!$R1 837
8 TraesCS5D01G057600 chr2B 723045637 723046173 536 False 826.0 826 94.424000 1455 1992 1 chr2B.!!$F1 537
9 TraesCS5D01G057600 chr2B 785072155 785072695 540 False 804.0 804 93.530000 1454 1992 1 chr2B.!!$F2 538
10 TraesCS5D01G057600 chr7B 17356772 17357310 538 True 813.0 813 93.878000 1454 1992 1 chr7B.!!$R1 538

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
122 128 0.041488 CGATAGGCCAGACGACGTAC 60.041 60.0 5.01 0.0 0.0 3.67 F
884 931 0.249531 TTCTACAGTTGCGTTGCGGA 60.250 50.0 0.00 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 4515 2.413765 GAGCCGATGGAGACGACC 59.586 66.667 0.00 0.0 0.00 4.79 R
2848 5480 0.028770 TTTCGCGGTGAACTGCTTTG 59.971 50.000 6.13 0.0 45.75 2.77 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
120 126 3.108343 CGATAGGCCAGACGACGT 58.892 61.111 5.01 0.00 0.00 4.34
121 127 2.314256 CGATAGGCCAGACGACGTA 58.686 57.895 5.01 0.00 0.00 3.57
122 128 0.041488 CGATAGGCCAGACGACGTAC 60.041 60.000 5.01 0.00 0.00 3.67
153 159 1.076533 ATGAACGCGGCAGTACGAAG 61.077 55.000 12.47 0.00 35.47 3.79
156 162 2.126618 CGCGGCAGTACGAAGTCA 60.127 61.111 0.00 0.00 43.93 3.41
157 163 2.434134 CGCGGCAGTACGAAGTCAC 61.434 63.158 0.00 0.00 43.93 3.67
158 164 2.434134 GCGGCAGTACGAAGTCACG 61.434 63.158 0.00 0.00 43.93 4.35
159 165 1.208358 CGGCAGTACGAAGTCACGA 59.792 57.895 0.00 0.00 43.93 4.35
160 166 0.386352 CGGCAGTACGAAGTCACGAA 60.386 55.000 0.00 0.00 43.93 3.85
161 167 1.058404 GGCAGTACGAAGTCACGAAC 58.942 55.000 0.00 0.00 43.93 3.95
162 168 1.335689 GGCAGTACGAAGTCACGAACT 60.336 52.381 0.00 0.00 43.93 3.01
163 169 1.977412 GCAGTACGAAGTCACGAACTC 59.023 52.381 0.00 0.00 43.93 3.01
164 170 2.582687 CAGTACGAAGTCACGAACTCC 58.417 52.381 0.00 0.00 43.93 3.85
165 171 2.031420 CAGTACGAAGTCACGAACTCCA 60.031 50.000 0.00 0.00 43.93 3.86
221 232 1.406898 GTTAGCTAGGGTGGTACCGTC 59.593 57.143 7.57 2.76 39.83 4.79
359 389 2.933287 CCACAGCCCACCTACCCA 60.933 66.667 0.00 0.00 0.00 4.51
365 403 0.770557 AGCCCACCTACCCAAACTGA 60.771 55.000 0.00 0.00 0.00 3.41
369 407 1.420138 CCACCTACCCAAACTGACAGT 59.580 52.381 1.07 1.07 0.00 3.55
852 899 3.552384 AGGTGGACGCGGGTTCAA 61.552 61.111 16.13 0.00 32.11 2.69
884 931 0.249531 TTCTACAGTTGCGTTGCGGA 60.250 50.000 0.00 0.00 0.00 5.54
897 944 1.254570 GTTGCGGATTTAGCTCGTACG 59.745 52.381 9.53 9.53 35.28 3.67
898 945 0.452987 TGCGGATTTAGCTCGTACGT 59.547 50.000 16.05 0.00 35.28 3.57
899 946 1.670295 TGCGGATTTAGCTCGTACGTA 59.330 47.619 16.05 0.00 35.28 3.57
900 947 2.291465 TGCGGATTTAGCTCGTACGTAT 59.709 45.455 16.05 5.07 35.28 3.06
901 948 2.655474 GCGGATTTAGCTCGTACGTATG 59.345 50.000 16.05 8.56 0.00 2.39
902 949 3.231965 CGGATTTAGCTCGTACGTATGG 58.768 50.000 16.05 6.89 0.00 2.74
903 950 3.058708 CGGATTTAGCTCGTACGTATGGA 60.059 47.826 16.05 6.99 0.00 3.41
904 951 4.474113 GGATTTAGCTCGTACGTATGGAG 58.526 47.826 16.05 16.30 0.00 3.86
905 952 4.023365 GGATTTAGCTCGTACGTATGGAGT 60.023 45.833 16.05 13.38 0.00 3.85
906 953 5.180117 GGATTTAGCTCGTACGTATGGAGTA 59.820 44.000 16.05 12.70 0.00 2.59
907 954 5.409643 TTTAGCTCGTACGTATGGAGTAC 57.590 43.478 16.05 10.36 40.59 2.73
908 955 3.191078 AGCTCGTACGTATGGAGTACT 57.809 47.619 16.05 0.00 41.51 2.73
909 956 2.871022 AGCTCGTACGTATGGAGTACTG 59.129 50.000 16.05 4.38 41.51 2.74
910 957 2.611292 GCTCGTACGTATGGAGTACTGT 59.389 50.000 16.05 0.00 41.51 3.55
911 958 3.545624 GCTCGTACGTATGGAGTACTGTG 60.546 52.174 16.05 3.32 41.51 3.66
914 961 2.941453 ACGTATGGAGTACTGTGCTG 57.059 50.000 0.00 0.00 0.00 4.41
917 964 2.796383 CGTATGGAGTACTGTGCTGCTC 60.796 54.545 17.16 7.93 0.00 4.26
922 969 1.135333 GAGTACTGTGCTGCTCCTACC 59.865 57.143 0.00 0.00 0.00 3.18
924 971 1.482593 GTACTGTGCTGCTCCTACCAT 59.517 52.381 0.00 0.00 0.00 3.55
1056 3604 1.696097 CCCCCTCCACCATTACTCCG 61.696 65.000 0.00 0.00 0.00 4.63
1952 4515 4.477975 GGCGTCGACGACCTCCTG 62.478 72.222 39.74 10.32 42.67 3.86
2036 4599 3.683937 GGCTGGCGCACACCAATT 61.684 61.111 10.83 0.00 39.86 2.32
2206 4774 7.352079 ACACCAAAAAGTTTCATCTCATCTT 57.648 32.000 0.00 0.00 0.00 2.40
2225 4793 4.584874 TCTTCCCATCAAAACGCATTCTA 58.415 39.130 0.00 0.00 0.00 2.10
2226 4794 5.007034 TCTTCCCATCAAAACGCATTCTAA 58.993 37.500 0.00 0.00 0.00 2.10
2237 4805 5.545658 AACGCATTCTAATAACTGTGGTG 57.454 39.130 0.00 0.00 0.00 4.17
2240 4808 3.947834 GCATTCTAATAACTGTGGTGGCT 59.052 43.478 0.00 0.00 0.00 4.75
2249 4829 0.466189 CTGTGGTGGCTGGTGAGTTT 60.466 55.000 0.00 0.00 0.00 2.66
2250 4830 0.751277 TGTGGTGGCTGGTGAGTTTG 60.751 55.000 0.00 0.00 0.00 2.93
2627 5216 1.338655 TGACACGACACGGATCAAGAA 59.661 47.619 0.00 0.00 0.00 2.52
2628 5217 2.223852 TGACACGACACGGATCAAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
2629 5218 2.993899 GACACGACACGGATCAAGAAAT 59.006 45.455 0.00 0.00 0.00 2.17
2630 5219 2.993899 ACACGACACGGATCAAGAAATC 59.006 45.455 0.00 0.00 0.00 2.17
2631 5220 2.028045 CACGACACGGATCAAGAAATCG 59.972 50.000 0.00 0.00 0.00 3.34
2632 5221 2.094906 ACGACACGGATCAAGAAATCGA 60.095 45.455 9.39 0.00 32.83 3.59
2633 5222 3.116300 CGACACGGATCAAGAAATCGAT 58.884 45.455 0.00 0.00 0.00 3.59
2664 5259 2.059345 GACGGGTCACCCTCCCAAAA 62.059 60.000 12.38 0.00 44.81 2.44
2714 5310 6.204108 ACAGAGGAATCGAAATGTTTTTACGT 59.796 34.615 0.00 0.00 0.00 3.57
2715 5311 7.075741 CAGAGGAATCGAAATGTTTTTACGTT 58.924 34.615 0.00 0.00 0.00 3.99
2718 5314 9.550811 GAGGAATCGAAATGTTTTTACGTTTAT 57.449 29.630 0.00 0.00 0.00 1.40
2750 5354 2.170166 CTCAGCTCTCCTCTGTTCTGT 58.830 52.381 0.00 0.00 33.48 3.41
2759 5363 1.912043 CCTCTGTTCTGTTCCCTCCAT 59.088 52.381 0.00 0.00 0.00 3.41
2817 5421 7.038729 CCCCTATGAAGTCAAGCTGATTCTATA 60.039 40.741 0.00 0.00 0.00 1.31
2818 5422 8.034215 CCCTATGAAGTCAAGCTGATTCTATAG 58.966 40.741 0.00 0.00 0.00 1.31
2819 5423 7.545265 CCTATGAAGTCAAGCTGATTCTATAGC 59.455 40.741 0.00 0.00 40.18 2.97
2875 5512 4.505191 GCAGTTCACCGCGAAATACTATAA 59.495 41.667 8.23 0.00 34.69 0.98
2878 5515 6.200286 CAGTTCACCGCGAAATACTATAATGT 59.800 38.462 8.23 0.00 34.69 2.71
2902 5539 6.365789 GTCCAAAATTGAAATCGAATGAGCAA 59.634 34.615 0.00 0.00 0.00 3.91
3129 5775 2.358582 CACGGCAAATGCATGATTAGGA 59.641 45.455 0.00 0.00 44.36 2.94
3165 5811 1.980765 TGTTGCTGAAGATGGTCTCCT 59.019 47.619 0.00 0.00 0.00 3.69
3218 5865 2.035442 GTCGAGGAGCAAGGGCAAC 61.035 63.158 0.00 0.00 44.61 4.17
3234 5881 1.195900 GCAACTTCAACGCGGTTCATA 59.804 47.619 12.47 0.00 0.00 2.15
3235 5882 2.350007 GCAACTTCAACGCGGTTCATAA 60.350 45.455 12.47 0.00 0.00 1.90
3236 5883 3.850374 GCAACTTCAACGCGGTTCATAAA 60.850 43.478 12.47 0.00 0.00 1.40
3237 5884 4.283678 CAACTTCAACGCGGTTCATAAAA 58.716 39.130 12.47 0.00 0.00 1.52
3238 5885 4.555348 ACTTCAACGCGGTTCATAAAAA 57.445 36.364 12.47 0.00 0.00 1.94
3259 5906 6.642707 AAAAAGACACCAAATATCGGTTCA 57.357 33.333 0.00 0.00 33.25 3.18
3260 5907 6.834168 AAAAGACACCAAATATCGGTTCAT 57.166 33.333 0.00 0.00 33.25 2.57
3261 5908 7.931578 AAAAGACACCAAATATCGGTTCATA 57.068 32.000 0.00 0.00 33.25 2.15
3262 5909 7.931578 AAAGACACCAAATATCGGTTCATAA 57.068 32.000 0.00 0.00 33.25 1.90
3263 5910 7.931578 AAGACACCAAATATCGGTTCATAAA 57.068 32.000 0.00 0.00 33.25 1.40
3287 5934 6.677781 AAACGGACATACCAAATATCAGTG 57.322 37.500 0.00 0.00 38.90 3.66
3294 5941 3.695830 ACCAAATATCAGTGGACACGT 57.304 42.857 6.97 0.00 38.36 4.49
3296 5943 4.394729 ACCAAATATCAGTGGACACGTTT 58.605 39.130 6.97 0.00 38.36 3.60
3302 5949 1.668751 TCAGTGGACACGTTTGAAAGC 59.331 47.619 0.00 0.00 36.20 3.51
3357 6004 8.621286 CATCTAAACCTATACACCAAAATGTCC 58.379 37.037 0.00 0.00 33.85 4.02
3361 6008 4.939439 ACCTATACACCAAAATGTCCGTTC 59.061 41.667 0.00 0.00 33.85 3.95
3367 6014 5.106442 ACACCAAAATGTCCGTTCTTTTTC 58.894 37.500 0.00 0.00 0.00 2.29
3368 6015 5.105752 CACCAAAATGTCCGTTCTTTTTCA 58.894 37.500 0.00 0.00 0.00 2.69
3370 6017 6.091441 CACCAAAATGTCCGTTCTTTTTCAAA 59.909 34.615 0.00 0.00 0.00 2.69
3371 6018 6.651225 ACCAAAATGTCCGTTCTTTTTCAAAA 59.349 30.769 0.00 0.00 0.00 2.44
3372 6019 7.173390 ACCAAAATGTCCGTTCTTTTTCAAAAA 59.827 29.630 0.00 0.00 0.00 1.94
3373 6020 8.180920 CCAAAATGTCCGTTCTTTTTCAAAAAT 58.819 29.630 0.00 0.00 0.00 1.82
3414 6061 1.202290 CCAAATGTCCGCTATGCAACC 60.202 52.381 0.00 0.00 0.00 3.77
3415 6062 1.745087 CAAATGTCCGCTATGCAACCT 59.255 47.619 0.00 0.00 0.00 3.50
3418 6065 0.391130 TGTCCGCTATGCAACCTCAC 60.391 55.000 0.00 0.00 0.00 3.51
3420 6067 0.175760 TCCGCTATGCAACCTCACTC 59.824 55.000 0.00 0.00 0.00 3.51
3434 6081 3.320541 ACCTCACTCTGAATCATCGATCC 59.679 47.826 0.00 0.00 0.00 3.36
3435 6082 3.563508 CTCACTCTGAATCATCGATCCG 58.436 50.000 0.00 0.00 0.00 4.18
3436 6083 2.952310 TCACTCTGAATCATCGATCCGT 59.048 45.455 0.00 0.00 0.00 4.69
3437 6084 4.134563 TCACTCTGAATCATCGATCCGTA 58.865 43.478 0.00 0.00 0.00 4.02
3438 6085 4.214332 TCACTCTGAATCATCGATCCGTAG 59.786 45.833 0.00 0.00 0.00 3.51
3439 6086 4.214332 CACTCTGAATCATCGATCCGTAGA 59.786 45.833 0.00 0.00 0.00 2.59
3440 6087 4.822350 ACTCTGAATCATCGATCCGTAGAA 59.178 41.667 0.00 0.00 0.00 2.10
3441 6088 5.109662 TCTGAATCATCGATCCGTAGAAC 57.890 43.478 0.00 0.00 0.00 3.01
3442 6089 4.023107 TCTGAATCATCGATCCGTAGAACC 60.023 45.833 0.00 0.00 0.00 3.62
3443 6090 3.889538 TGAATCATCGATCCGTAGAACCT 59.110 43.478 0.00 0.00 0.00 3.50
3444 6091 5.067954 TGAATCATCGATCCGTAGAACCTA 58.932 41.667 0.00 0.00 0.00 3.08
3524 6179 9.740239 CATCGATTTCCAAATTCAATCATACTT 57.260 29.630 0.00 0.00 0.00 2.24
3527 6182 9.793252 CGATTTCCAAATTCAATCATACTTCTT 57.207 29.630 0.00 0.00 0.00 2.52
3548 6203 3.316283 TGAAAGCGGCATTCATTTCAAC 58.684 40.909 15.84 0.00 38.38 3.18
3551 6206 1.895131 AGCGGCATTCATTTCAACCTT 59.105 42.857 1.45 0.00 0.00 3.50
3561 6216 5.047566 TCATTTCAACCTTTCACTCCTCA 57.952 39.130 0.00 0.00 0.00 3.86
3562 6217 5.445069 TCATTTCAACCTTTCACTCCTCAA 58.555 37.500 0.00 0.00 0.00 3.02
3570 6225 3.251972 CCTTTCACTCCTCAAGCTTGAAC 59.748 47.826 28.16 0.00 36.64 3.18
3583 6238 5.824624 TCAAGCTTGAACTTCTTCATCAACT 59.175 36.000 26.61 0.00 36.26 3.16
3590 6245 8.675705 TTGAACTTCTTCATCAACTCATGTTA 57.324 30.769 0.00 0.00 36.26 2.41
3608 6263 7.394016 TCATGTTATTCACCTAGATGTTGTGT 58.606 34.615 0.00 0.00 0.00 3.72
3617 6272 2.191128 AGATGTTGTGTCCCTTGAGC 57.809 50.000 0.00 0.00 0.00 4.26
3620 6275 2.435372 TGTTGTGTCCCTTGAGCTTT 57.565 45.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 129 2.126888 CGTTCATGGTTGCGGCAC 60.127 61.111 0.05 0.00 0.00 5.01
130 136 1.004320 TACTGCCGCGTTCATGGTT 60.004 52.632 4.92 0.00 0.00 3.67
153 159 2.351544 GGTAGACTGTGGAGTTCGTGAC 60.352 54.545 0.00 0.00 30.16 3.67
156 162 0.879765 CGGTAGACTGTGGAGTTCGT 59.120 55.000 0.00 0.00 30.16 3.85
157 163 0.456312 GCGGTAGACTGTGGAGTTCG 60.456 60.000 0.00 0.00 30.16 3.95
158 164 0.601558 TGCGGTAGACTGTGGAGTTC 59.398 55.000 0.00 0.00 30.16 3.01
159 165 0.317479 GTGCGGTAGACTGTGGAGTT 59.683 55.000 0.00 0.00 30.16 3.01
160 166 0.539901 AGTGCGGTAGACTGTGGAGT 60.540 55.000 0.00 0.00 33.98 3.85
161 167 1.402259 CTAGTGCGGTAGACTGTGGAG 59.598 57.143 0.00 0.00 0.00 3.86
162 168 1.003928 TCTAGTGCGGTAGACTGTGGA 59.996 52.381 0.00 0.00 0.00 4.02
163 169 1.460504 TCTAGTGCGGTAGACTGTGG 58.539 55.000 0.00 0.00 0.00 4.17
164 170 2.683362 TGATCTAGTGCGGTAGACTGTG 59.317 50.000 0.00 0.00 31.75 3.66
165 171 3.000684 TGATCTAGTGCGGTAGACTGT 57.999 47.619 0.00 0.00 31.75 3.55
359 389 2.594592 GGCCCGCACTGTCAGTTT 60.595 61.111 1.67 0.00 0.00 2.66
737 775 2.027073 GCTGACACGCGATCCACAA 61.027 57.895 15.93 0.00 0.00 3.33
819 857 4.511246 CTGGGTGGCCATGCGGAT 62.511 66.667 9.72 0.00 0.00 4.18
852 899 5.739358 GCAACTGTAGAAGGCGTATTCCTAT 60.739 44.000 0.00 0.00 34.82 2.57
884 931 5.762218 AGTACTCCATACGTACGAGCTAAAT 59.238 40.000 24.41 4.94 41.51 1.40
897 944 2.482142 GGAGCAGCACAGTACTCCATAC 60.482 54.545 0.00 0.00 46.57 2.39
898 945 1.757118 GGAGCAGCACAGTACTCCATA 59.243 52.381 0.00 0.00 46.57 2.74
899 946 0.539051 GGAGCAGCACAGTACTCCAT 59.461 55.000 0.00 0.00 46.57 3.41
900 947 1.975327 GGAGCAGCACAGTACTCCA 59.025 57.895 0.00 0.00 46.57 3.86
901 948 4.921834 GGAGCAGCACAGTACTCC 57.078 61.111 0.00 0.00 41.81 3.85
902 949 1.135333 GGTAGGAGCAGCACAGTACTC 59.865 57.143 0.00 0.00 0.00 2.59
903 950 1.187087 GGTAGGAGCAGCACAGTACT 58.813 55.000 0.00 0.00 0.00 2.73
904 951 0.895530 TGGTAGGAGCAGCACAGTAC 59.104 55.000 0.00 0.00 0.00 2.73
905 952 1.866015 ATGGTAGGAGCAGCACAGTA 58.134 50.000 0.00 0.00 0.00 2.74
906 953 0.987294 AATGGTAGGAGCAGCACAGT 59.013 50.000 0.00 0.00 0.00 3.55
907 954 1.339438 ACAATGGTAGGAGCAGCACAG 60.339 52.381 0.00 0.00 0.00 3.66
908 955 0.692476 ACAATGGTAGGAGCAGCACA 59.308 50.000 0.00 0.00 0.00 4.57
909 956 2.555199 CTACAATGGTAGGAGCAGCAC 58.445 52.381 0.00 0.00 42.71 4.40
910 957 1.134401 GCTACAATGGTAGGAGCAGCA 60.134 52.381 9.38 0.00 45.82 4.41
911 958 1.587547 GCTACAATGGTAGGAGCAGC 58.412 55.000 9.38 0.00 45.82 5.25
914 961 1.854227 GACGCTACAATGGTAGGAGC 58.146 55.000 9.38 0.00 45.82 4.70
917 964 1.404391 AGACGACGCTACAATGGTAGG 59.596 52.381 9.38 2.30 45.82 3.18
922 969 1.828832 GGAGAGACGACGCTACAATG 58.171 55.000 0.00 0.00 0.00 2.82
924 971 0.671472 TCGGAGAGACGACGCTACAA 60.671 55.000 1.62 0.00 38.06 2.41
1952 4515 2.413765 GAGCCGATGGAGACGACC 59.586 66.667 0.00 0.00 0.00 4.79
2206 4774 6.601613 AGTTATTAGAATGCGTTTTGATGGGA 59.398 34.615 0.00 0.00 0.00 4.37
2225 4793 1.423541 TCACCAGCCACCACAGTTATT 59.576 47.619 0.00 0.00 0.00 1.40
2226 4794 1.003580 CTCACCAGCCACCACAGTTAT 59.996 52.381 0.00 0.00 0.00 1.89
2237 4805 0.890996 CCTGGACAAACTCACCAGCC 60.891 60.000 0.00 0.00 46.65 4.85
2240 4808 0.179020 CAGCCTGGACAAACTCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2588 5177 4.662961 TGCCGTGAGTCCTGCGTG 62.663 66.667 0.00 0.00 0.00 5.34
2627 5216 0.102300 TCCACGTCGCATGATCGATT 59.898 50.000 0.00 0.00 40.84 3.34
2628 5217 0.595053 GTCCACGTCGCATGATCGAT 60.595 55.000 0.00 0.00 40.84 3.59
2629 5218 1.226575 GTCCACGTCGCATGATCGA 60.227 57.895 0.00 0.00 35.95 3.59
2630 5219 2.568031 CGTCCACGTCGCATGATCG 61.568 63.158 0.00 0.00 34.11 3.69
2631 5220 2.230940 CCGTCCACGTCGCATGATC 61.231 63.158 0.00 0.00 37.74 2.92
2632 5221 2.202743 CCGTCCACGTCGCATGAT 60.203 61.111 0.00 0.00 37.74 2.45
2633 5222 4.429212 CCCGTCCACGTCGCATGA 62.429 66.667 0.00 0.00 37.74 3.07
2664 5259 1.555967 AGGCGGGCAATGTACAAAAT 58.444 45.000 0.00 0.00 0.00 1.82
2718 5314 8.811017 CAGAGGAGAGCTGAGGATAATAATAAA 58.189 37.037 0.00 0.00 35.39 1.40
2720 5316 7.474445 ACAGAGGAGAGCTGAGGATAATAATA 58.526 38.462 0.00 0.00 36.86 0.98
2722 5318 5.710646 ACAGAGGAGAGCTGAGGATAATAA 58.289 41.667 0.00 0.00 36.86 1.40
2723 5319 5.332106 ACAGAGGAGAGCTGAGGATAATA 57.668 43.478 0.00 0.00 36.86 0.98
2724 5320 4.197559 ACAGAGGAGAGCTGAGGATAAT 57.802 45.455 0.00 0.00 36.86 1.28
2733 5337 1.899142 GGAACAGAACAGAGGAGAGCT 59.101 52.381 0.00 0.00 0.00 4.09
2750 5354 2.721167 CGGCGACTCATGGAGGGAA 61.721 63.158 0.00 0.00 33.35 3.97
2759 5363 2.261361 CCACATGTCGGCGACTCA 59.739 61.111 36.17 20.99 33.15 3.41
2817 5421 1.344438 TCGACAAAGTGGATGTGAGCT 59.656 47.619 0.00 0.00 0.00 4.09
2818 5422 1.728971 CTCGACAAAGTGGATGTGAGC 59.271 52.381 0.00 0.00 0.00 4.26
2819 5423 2.733552 CACTCGACAAAGTGGATGTGAG 59.266 50.000 0.00 0.00 42.42 3.51
2820 5424 2.364002 TCACTCGACAAAGTGGATGTGA 59.636 45.455 4.36 8.88 45.47 3.58
2822 5426 2.755650 GTCACTCGACAAAGTGGATGT 58.244 47.619 4.36 0.00 45.47 3.06
2848 5480 0.028770 TTTCGCGGTGAACTGCTTTG 59.971 50.000 6.13 0.00 45.75 2.77
2875 5512 6.532657 GCTCATTCGATTTCAATTTTGGACAT 59.467 34.615 0.00 0.00 0.00 3.06
2878 5515 6.023357 TGCTCATTCGATTTCAATTTTGGA 57.977 33.333 0.00 0.00 0.00 3.53
2902 5539 4.242475 ACACATTGACACATCGTATTCGT 58.758 39.130 0.00 0.00 38.33 3.85
3071 5709 6.316140 ACATTGCAATCGATCAAGCTACTAAA 59.684 34.615 9.53 4.95 0.00 1.85
3104 5750 0.957362 TCATGCATTTGCCGTGTGAA 59.043 45.000 0.00 0.00 41.18 3.18
3165 5811 6.542370 ACAATCAGGAAACGAAAAGAAGAAGA 59.458 34.615 0.00 0.00 0.00 2.87
3209 5856 1.370414 CGCGTTGAAGTTGCCCTTG 60.370 57.895 0.00 0.00 32.03 3.61
3236 5883 6.642707 TGAACCGATATTTGGTGTCTTTTT 57.357 33.333 1.69 0.00 40.35 1.94
3237 5884 6.834168 ATGAACCGATATTTGGTGTCTTTT 57.166 33.333 1.69 0.00 40.35 2.27
3238 5885 7.931578 TTATGAACCGATATTTGGTGTCTTT 57.068 32.000 1.69 0.00 40.35 2.52
3239 5886 7.931578 TTTATGAACCGATATTTGGTGTCTT 57.068 32.000 1.69 3.94 40.35 3.01
3240 5887 7.931578 TTTTATGAACCGATATTTGGTGTCT 57.068 32.000 1.69 0.00 40.35 3.41
3262 5909 7.362574 CCACTGATATTTGGTATGTCCGTTTTT 60.363 37.037 0.00 0.00 39.52 1.94
3263 5910 6.094881 CCACTGATATTTGGTATGTCCGTTTT 59.905 38.462 0.00 0.00 39.52 2.43
3273 5920 4.811969 ACGTGTCCACTGATATTTGGTA 57.188 40.909 0.00 0.00 34.19 3.25
3283 5930 1.594518 CGCTTTCAAACGTGTCCACTG 60.595 52.381 0.00 0.00 0.00 3.66
3284 5931 0.655733 CGCTTTCAAACGTGTCCACT 59.344 50.000 0.00 0.00 0.00 4.00
3287 5934 1.843753 CAAACGCTTTCAAACGTGTCC 59.156 47.619 0.00 0.00 42.68 4.02
3294 5941 2.786578 GCAATCGACAAACGCTTTCAAA 59.213 40.909 0.00 0.00 42.26 2.69
3296 5943 1.658931 CGCAATCGACAAACGCTTTCA 60.659 47.619 0.00 0.00 42.26 2.69
3302 5949 1.257936 CCTATCCGCAATCGACAAACG 59.742 52.381 0.00 0.00 44.09 3.60
3379 6026 8.238631 GCGGACATTTGGTTTAGTTTTATTCTA 58.761 33.333 0.00 0.00 0.00 2.10
3393 6040 1.472480 GTTGCATAGCGGACATTTGGT 59.528 47.619 0.00 0.00 0.00 3.67
3403 6050 1.134995 TCAGAGTGAGGTTGCATAGCG 60.135 52.381 0.00 0.00 0.00 4.26
3414 6061 3.004210 ACGGATCGATGATTCAGAGTGAG 59.996 47.826 0.54 0.00 0.00 3.51
3415 6062 2.952310 ACGGATCGATGATTCAGAGTGA 59.048 45.455 0.54 0.00 0.00 3.41
3418 6065 5.150683 GTTCTACGGATCGATGATTCAGAG 58.849 45.833 0.54 0.00 0.00 3.35
3420 6067 4.022762 AGGTTCTACGGATCGATGATTCAG 60.023 45.833 0.54 0.00 0.00 3.02
3494 6144 7.784037 TGATTGAATTTGGAAATCGATGGATT 58.216 30.769 0.00 0.00 44.69 3.01
3495 6145 7.350744 TGATTGAATTTGGAAATCGATGGAT 57.649 32.000 0.00 0.00 33.83 3.41
3497 6147 8.355169 AGTATGATTGAATTTGGAAATCGATGG 58.645 33.333 0.00 0.00 33.83 3.51
3498 6148 9.740239 AAGTATGATTGAATTTGGAAATCGATG 57.260 29.630 0.00 0.00 33.83 3.84
3500 6150 9.177608 AGAAGTATGATTGAATTTGGAAATCGA 57.822 29.630 0.00 0.00 33.83 3.59
3501 6151 9.793252 AAGAAGTATGATTGAATTTGGAAATCG 57.207 29.630 0.00 0.00 33.83 3.34
3514 6169 4.142622 TGCCGCTTTCAAGAAGTATGATTG 60.143 41.667 0.00 0.00 0.00 2.67
3524 6179 3.255395 TGAAATGAATGCCGCTTTCAAGA 59.745 39.130 21.53 7.01 36.72 3.02
3527 6182 3.316283 GTTGAAATGAATGCCGCTTTCA 58.684 40.909 20.36 20.36 37.49 2.69
3548 6203 3.131709 TCAAGCTTGAGGAGTGAAAGG 57.868 47.619 25.16 0.00 32.50 3.11
3551 6206 3.845781 AGTTCAAGCTTGAGGAGTGAA 57.154 42.857 27.02 9.80 38.61 3.18
3561 6216 5.824624 TGAGTTGATGAAGAAGTTCAAGCTT 59.175 36.000 5.50 0.00 45.88 3.74
3562 6217 5.371526 TGAGTTGATGAAGAAGTTCAAGCT 58.628 37.500 5.50 0.00 45.88 3.74
3570 6225 8.180267 GGTGAATAACATGAGTTGATGAAGAAG 58.820 37.037 0.00 0.00 38.69 2.85
3583 6238 7.394016 ACACAACATCTAGGTGAATAACATGA 58.606 34.615 10.76 0.00 36.95 3.07
3590 6245 3.846588 AGGGACACAACATCTAGGTGAAT 59.153 43.478 10.76 0.00 36.95 2.57


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

AutoCloner maintained by Alex Coulton.