Multiple sequence alignment - TraesCS4D01G110800

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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 TraesCS4D01G110800 chr4D 100.000 4421 0 0 1 4421 91226860 91222440 0.000000e+00 8165
1 TraesCS4D01G110800 chr4A 94.772 3022 121 16 558 3554 503619301 503616292 0.000000e+00 4671
2 TraesCS4D01G110800 chr4A 96.600 647 18 3 3548 4194 503616218 503615576 0.000000e+00 1070
3 TraesCS4D01G110800 chr4A 88.778 499 26 8 1 498 503619763 503619294 6.370000e-163 584
4 TraesCS4D01G110800 chr4B 94.036 3035 121 22 558 3554 128027822 128024810 0.000000e+00 4547
5 TraesCS4D01G110800 chr4B 96.224 874 19 4 3548 4421 128024698 128023839 0.000000e+00 1419
6 TraesCS4D01G110800 chr4B 94.236 347 19 1 152 498 128028160 128027815 3.030000e-146 529
7 TraesCS4D01G110800 chr4B 92.982 114 8 0 1 114 128028275 128028162 2.740000e-37 167


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 TraesCS4D01G110800 chr4D 91222440 91226860 4420 True 8165.000000 8165 100.000000 1 4421 1 chr4D.!!$R1 4420
1 TraesCS4D01G110800 chr4A 503615576 503619763 4187 True 2108.333333 4671 93.383333 1 4194 3 chr4A.!!$R1 4193
2 TraesCS4D01G110800 chr4B 128023839 128028275 4436 True 1665.500000 4547 94.369500 1 4421 4 chr4B.!!$R1 4420

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
990 1002 1.009829 CAATCTCCCGCTGTTGCTAC 58.990 55.0 0.00 0.0 36.97 3.58 F
1298 1336 0.179020 TGGGAGCAAGTTGGTGTCAG 60.179 55.0 13.24 0.0 0.00 3.51 F
2652 2691 0.677288 TCGTCGACCTGAACATTGGT 59.323 50.0 10.58 0.0 39.60 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2908 2947 0.890683 AGCAACTTGTAAGGCATGCC 59.109 50.000 30.12 30.12 35.91 4.40 R
3013 3052 1.153804 GAGACGCCTCCTTTCCGAC 60.154 63.158 0.00 0.00 33.30 4.79 R
3678 3834 0.179056 ACTGGTTGACACCTGGTTCG 60.179 55.000 0.00 0.00 44.56 3.95 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
69 70 5.602145 AGCTCTCTATTATCAGCTTCAACCT 59.398 40.000 0.00 0.00 39.22 3.50
137 138 1.531149 GCGTGGTCATTGGATATTCGG 59.469 52.381 0.00 0.00 0.00 4.30
170 171 6.772716 ACTCAGGAATAGTTCAAGAGCAAAAA 59.227 34.615 9.22 0.00 36.30 1.94
344 345 5.092554 TGCCGTCCTTAACTCATTTGATA 57.907 39.130 0.00 0.00 0.00 2.15
349 350 7.210174 CCGTCCTTAACTCATTTGATATCAGA 58.790 38.462 5.39 1.40 0.00 3.27
370 371 2.089980 GAGCATGTTTCCTGAGCATGT 58.910 47.619 12.23 3.83 41.27 3.21
373 374 4.081406 AGCATGTTTCCTGAGCATGTTAA 58.919 39.130 12.23 0.00 41.27 2.01
404 405 4.094294 CGTCGTTGACAAAATGGACCATAT 59.906 41.667 7.59 0.00 32.09 1.78
417 418 5.304686 TGGACCATATAACCATTCCTGTC 57.695 43.478 0.00 0.00 0.00 3.51
457 458 7.763613 AGGAATTAATTTGAGCCCTCTATGAT 58.236 34.615 1.43 0.00 0.00 2.45
468 469 5.374921 AGCCCTCTATGATGAAATCTTGTG 58.625 41.667 0.00 0.00 45.81 3.33
496 497 3.984090 TGGTGGGGGCATATGATACTTAA 59.016 43.478 6.97 0.00 0.00 1.85
497 498 4.605813 TGGTGGGGGCATATGATACTTAAT 59.394 41.667 6.97 0.00 0.00 1.40
498 499 5.793237 TGGTGGGGGCATATGATACTTAATA 59.207 40.000 6.97 0.00 0.00 0.98
499 500 6.069673 TGGTGGGGGCATATGATACTTAATAG 60.070 42.308 6.97 0.00 0.00 1.73
500 501 5.823045 GTGGGGGCATATGATACTTAATAGC 59.177 44.000 6.97 0.00 0.00 2.97
501 502 5.731187 TGGGGGCATATGATACTTAATAGCT 59.269 40.000 6.97 0.00 0.00 3.32
502 503 6.126768 TGGGGGCATATGATACTTAATAGCTC 60.127 42.308 6.97 0.00 0.00 4.09
503 504 6.100424 GGGGGCATATGATACTTAATAGCTCT 59.900 42.308 6.97 0.00 0.00 4.09
504 505 7.290248 GGGGGCATATGATACTTAATAGCTCTA 59.710 40.741 6.97 0.00 0.00 2.43
505 506 8.705594 GGGGCATATGATACTTAATAGCTCTAA 58.294 37.037 6.97 0.00 0.00 2.10
524 525 9.323985 AGCTCTAATTATTCAGATTTGTGACTC 57.676 33.333 0.00 0.00 0.00 3.36
525 526 9.323985 GCTCTAATTATTCAGATTTGTGACTCT 57.676 33.333 0.00 0.00 0.00 3.24
527 528 9.823647 TCTAATTATTCAGATTTGTGACTCTCC 57.176 33.333 0.00 0.00 0.00 3.71
528 529 9.829507 CTAATTATTCAGATTTGTGACTCTCCT 57.170 33.333 0.00 0.00 0.00 3.69
530 531 8.729805 ATTATTCAGATTTGTGACTCTCCTTC 57.270 34.615 0.00 0.00 0.00 3.46
531 532 4.543590 TCAGATTTGTGACTCTCCTTCC 57.456 45.455 0.00 0.00 0.00 3.46
532 533 4.163427 TCAGATTTGTGACTCTCCTTCCT 58.837 43.478 0.00 0.00 0.00 3.36
533 534 4.221703 TCAGATTTGTGACTCTCCTTCCTC 59.778 45.833 0.00 0.00 0.00 3.71
534 535 3.517500 AGATTTGTGACTCTCCTTCCTCC 59.482 47.826 0.00 0.00 0.00 4.30
535 536 2.704190 TTGTGACTCTCCTTCCTCCT 57.296 50.000 0.00 0.00 0.00 3.69
536 537 1.930251 TGTGACTCTCCTTCCTCCTG 58.070 55.000 0.00 0.00 0.00 3.86
537 538 1.148027 TGTGACTCTCCTTCCTCCTGT 59.852 52.381 0.00 0.00 0.00 4.00
538 539 1.548269 GTGACTCTCCTTCCTCCTGTG 59.452 57.143 0.00 0.00 0.00 3.66
539 540 1.429299 TGACTCTCCTTCCTCCTGTGA 59.571 52.381 0.00 0.00 0.00 3.58
540 541 2.158310 TGACTCTCCTTCCTCCTGTGAA 60.158 50.000 0.00 0.00 0.00 3.18
541 542 2.900546 GACTCTCCTTCCTCCTGTGAAA 59.099 50.000 0.00 0.00 0.00 2.69
542 543 3.318313 ACTCTCCTTCCTCCTGTGAAAA 58.682 45.455 0.00 0.00 0.00 2.29
543 544 3.071747 ACTCTCCTTCCTCCTGTGAAAAC 59.928 47.826 0.00 0.00 0.00 2.43
544 545 3.045634 TCTCCTTCCTCCTGTGAAAACA 58.954 45.455 0.00 0.00 0.00 2.83
545 546 3.652869 TCTCCTTCCTCCTGTGAAAACAT 59.347 43.478 0.00 0.00 0.00 2.71
546 547 3.754965 TCCTTCCTCCTGTGAAAACATG 58.245 45.455 0.00 0.00 0.00 3.21
547 548 3.138283 TCCTTCCTCCTGTGAAAACATGT 59.862 43.478 0.00 0.00 0.00 3.21
548 549 3.891366 CCTTCCTCCTGTGAAAACATGTT 59.109 43.478 4.92 4.92 0.00 2.71
549 550 4.342092 CCTTCCTCCTGTGAAAACATGTTT 59.658 41.667 18.13 18.13 0.00 2.83
550 551 5.534654 CCTTCCTCCTGTGAAAACATGTTTA 59.465 40.000 23.53 6.97 31.63 2.01
551 552 6.209391 CCTTCCTCCTGTGAAAACATGTTTAT 59.791 38.462 23.53 13.74 31.63 1.40
552 553 7.255942 CCTTCCTCCTGTGAAAACATGTTTATT 60.256 37.037 23.53 9.72 31.63 1.40
553 554 8.698973 TTCCTCCTGTGAAAACATGTTTATTA 57.301 30.769 23.53 10.53 31.63 0.98
554 555 8.877864 TCCTCCTGTGAAAACATGTTTATTAT 57.122 30.769 23.53 8.58 31.63 1.28
555 556 9.967451 TCCTCCTGTGAAAACATGTTTATTATA 57.033 29.630 23.53 10.49 31.63 0.98
604 605 3.565482 CAGTTGTACTGCTGGTTGTGATT 59.435 43.478 8.68 0.00 39.62 2.57
634 635 3.259064 CATGCTGCCAAGATCCTTTTTG 58.741 45.455 0.00 0.00 0.00 2.44
689 690 4.814771 GCACTCTTACAGTTGTACTTTGGT 59.185 41.667 0.00 0.00 30.26 3.67
696 697 9.485206 TCTTACAGTTGTACTTTGGTATCTTTC 57.515 33.333 0.00 0.00 0.00 2.62
699 700 6.935208 ACAGTTGTACTTTGGTATCTTTCTCC 59.065 38.462 0.00 0.00 0.00 3.71
707 708 7.518188 ACTTTGGTATCTTTCTCCTTTTCTGA 58.482 34.615 0.00 0.00 0.00 3.27
717 718 4.307432 TCTCCTTTTCTGATCGAACACAC 58.693 43.478 0.00 0.00 0.00 3.82
723 724 6.072728 CCTTTTCTGATCGAACACACCAATAA 60.073 38.462 0.00 0.00 0.00 1.40
727 728 4.196193 TGATCGAACACACCAATAATCCC 58.804 43.478 0.00 0.00 0.00 3.85
773 774 3.750130 ACTCTTGACAATGTGCAGATGTC 59.250 43.478 15.87 15.87 42.90 3.06
858 865 3.191078 GGAATCATCCAGACACTCCTG 57.809 52.381 0.00 0.00 45.79 3.86
867 874 3.576118 TCCAGACACTCCTGAGAGAAAAG 59.424 47.826 0.22 0.00 43.39 2.27
870 877 5.279910 CCAGACACTCCTGAGAGAAAAGAAT 60.280 44.000 0.22 0.00 43.39 2.40
871 878 5.868801 CAGACACTCCTGAGAGAAAAGAATC 59.131 44.000 0.22 0.00 43.39 2.52
955 967 4.357918 AGTCAGTGGAAAGCTGTACATT 57.642 40.909 0.00 0.00 35.60 2.71
979 991 2.629336 GACTCCATCCACAATCTCCC 57.371 55.000 0.00 0.00 0.00 4.30
987 999 1.503542 CACAATCTCCCGCTGTTGC 59.496 57.895 0.00 0.00 0.00 4.17
990 1002 1.009829 CAATCTCCCGCTGTTGCTAC 58.990 55.000 0.00 0.00 36.97 3.58
997 1009 1.608025 CCCGCTGTTGCTACTTTCTGA 60.608 52.381 0.00 0.00 36.97 3.27
1001 1013 4.320494 CCGCTGTTGCTACTTTCTGAAAAT 60.320 41.667 4.18 0.00 36.97 1.82
1041 1053 1.901650 GCGTGAAGGCAGGAGAAACG 61.902 60.000 0.00 0.00 31.73 3.60
1086 1098 1.815003 CTGGAACCAGGAAATCTGTGC 59.185 52.381 12.54 0.00 41.83 4.57
1091 1103 2.044946 AGGAAATCTGTGCGGCCC 60.045 61.111 0.00 0.00 0.00 5.80
1135 1147 2.079925 CTTTGCAACAGCTCTACTCCC 58.920 52.381 0.00 0.00 0.00 4.30
1137 1149 0.898320 TGCAACAGCTCTACTCCCTC 59.102 55.000 0.00 0.00 0.00 4.30
1153 1165 1.602311 CCTCAGACAAGCAGCTTTGT 58.398 50.000 4.38 7.42 43.61 2.83
1154 1166 2.550855 CCCTCAGACAAGCAGCTTTGTA 60.551 50.000 4.38 0.00 41.15 2.41
1158 1170 3.133691 CAGACAAGCAGCTTTGTACTCA 58.866 45.455 4.38 0.00 41.15 3.41
1167 1179 6.903419 AGCAGCTTTGTACTCATTTAGTTTC 58.097 36.000 0.00 0.00 39.80 2.78
1168 1180 5.790495 GCAGCTTTGTACTCATTTAGTTTCG 59.210 40.000 0.00 0.00 39.80 3.46
1209 1221 6.899089 TCATAACTCCATTAGAATCTGCCAA 58.101 36.000 0.00 0.00 0.00 4.52
1231 1243 9.083080 GCCAAATAATTTGTATCACCTTACAAC 57.917 33.333 0.00 0.00 40.74 3.32
1238 1250 5.506730 TGTATCACCTTACAACAATGGGA 57.493 39.130 0.00 0.00 0.00 4.37
1298 1336 0.179020 TGGGAGCAAGTTGGTGTCAG 60.179 55.000 13.24 0.00 0.00 3.51
1410 1448 7.817478 ACGTCAACATTAATTCTGTATCAGACA 59.183 33.333 0.00 0.00 40.46 3.41
1525 1563 1.812571 CTAGGTCGCATTTTGTTGCCT 59.187 47.619 0.00 0.00 39.52 4.75
1820 1859 3.521126 ACCTCTAGCTCAATCCATGTTGT 59.479 43.478 0.00 0.00 0.00 3.32
1897 1936 5.306937 TCCACACATTCTCTTTTCTCCACTA 59.693 40.000 0.00 0.00 0.00 2.74
1898 1937 5.409826 CCACACATTCTCTTTTCTCCACTAC 59.590 44.000 0.00 0.00 0.00 2.73
1899 1938 6.226787 CACACATTCTCTTTTCTCCACTACT 58.773 40.000 0.00 0.00 0.00 2.57
1900 1939 7.378966 CACACATTCTCTTTTCTCCACTACTA 58.621 38.462 0.00 0.00 0.00 1.82
1901 1940 7.543868 CACACATTCTCTTTTCTCCACTACTAG 59.456 40.741 0.00 0.00 0.00 2.57
1902 1941 7.233757 ACACATTCTCTTTTCTCCACTACTAGT 59.766 37.037 0.00 0.00 0.00 2.57
2162 2201 1.668419 GTGTTCTTGGACACTGCAGT 58.332 50.000 15.25 15.25 44.99 4.40
2334 2373 3.560251 ACTGGTGCAGAGGCGGTT 61.560 61.111 0.00 0.00 45.35 4.44
2373 2412 1.165907 TTGCCTTGGCAGTGTTCTCG 61.166 55.000 14.33 0.00 0.00 4.04
2538 2577 3.872696 TGATAGAATGTCGGTGCAACAT 58.127 40.909 0.98 0.00 39.98 2.71
2632 2671 1.024046 GGGCGATACACATGTGCACA 61.024 55.000 25.68 24.08 0.00 4.57
2652 2691 0.677288 TCGTCGACCTGAACATTGGT 59.323 50.000 10.58 0.00 39.60 3.67
2747 2786 1.515088 CAGCAGACGCCGACTACAG 60.515 63.158 0.00 0.00 39.83 2.74
2808 2847 1.004918 CGCGGACTCCTTGAACCTT 60.005 57.895 0.00 0.00 0.00 3.50
2811 2850 0.977395 CGGACTCCTTGAACCTTCCT 59.023 55.000 0.00 0.00 0.00 3.36
2890 2929 1.207329 ACTGTAAAGGCTCGGTGATCC 59.793 52.381 0.00 0.00 0.00 3.36
2898 2937 0.749649 GCTCGGTGATCCTCTCATGT 59.250 55.000 0.00 0.00 35.97 3.21
2908 2947 3.391506 TCCTCTCATGTGACACAACAG 57.608 47.619 13.23 11.17 32.52 3.16
3013 3052 3.314080 CGTAGAAGAGGAGCTGGTTAGAG 59.686 52.174 0.00 0.00 0.00 2.43
3115 3154 2.047465 CACTGGCGAGCTGCTTCT 60.047 61.111 2.53 0.00 45.43 2.85
3229 3268 2.894126 ACAGTTGAGGTCACTACTCCTG 59.106 50.000 0.00 0.00 33.83 3.86
3230 3269 2.894126 CAGTTGAGGTCACTACTCCTGT 59.106 50.000 0.00 0.00 33.83 4.00
3267 3306 1.968540 GGCTTGTGACCTGAGTGGC 60.969 63.158 0.00 0.00 40.22 5.01
3411 3450 5.640147 TGGGCTCCAATCTTAAAAGAAAGA 58.360 37.500 0.00 0.00 38.77 2.52
3433 3472 6.835914 AGAAGCTCATGACGTTCTTTATTTG 58.164 36.000 8.44 0.00 0.00 2.32
3502 3541 4.042311 TGGTTAGTGAGCCACCTTATTTGA 59.958 41.667 2.18 0.00 34.49 2.69
3507 3546 4.396166 AGTGAGCCACCTTATTTGATTTCG 59.604 41.667 2.18 0.00 34.49 3.46
3602 3758 6.211584 AGTCTCAAGTAGCAAGTGGAAGAATA 59.788 38.462 0.00 0.00 0.00 1.75
3767 3923 4.262420 GCCCAAGTTGTATTGAAACCATGT 60.262 41.667 1.45 0.00 31.55 3.21
3768 3924 5.741673 GCCCAAGTTGTATTGAAACCATGTT 60.742 40.000 1.45 0.00 31.55 2.71
3963 4119 2.834549 GGACTGATTGGAGACTTCCTCA 59.165 50.000 0.00 0.00 44.36 3.86
3964 4120 3.454082 GGACTGATTGGAGACTTCCTCAT 59.546 47.826 0.00 0.00 44.36 2.90
4225 4381 1.018148 CGTCTCAGCTCAGTACGGAT 58.982 55.000 0.00 0.00 0.00 4.18
4334 4490 3.643320 TGATGATCGTAGAAGGCTGGAAT 59.357 43.478 0.00 0.00 43.58 3.01
4355 4511 1.621317 TCGTGTTGCTAAGGATCCACA 59.379 47.619 15.82 5.30 0.00 4.17
4379 4535 0.768221 TGTTGAGGAAGCAGAGGGGT 60.768 55.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.397941 TGGCAGAGGTCAGAAGGTTG 59.602 55.000 0.00 0.00 0.00 3.77
69 70 1.131638 ACAAGTGGCAGAGGTCAGAA 58.868 50.000 0.00 0.00 0.00 3.02
137 138 3.567478 ACTATTCCTGAGTGGGCAATC 57.433 47.619 0.00 0.00 36.20 2.67
260 261 4.573900 CACTGACTACTGGAGAAGCAAAT 58.426 43.478 0.00 0.00 0.00 2.32
264 265 1.548269 AGCACTGACTACTGGAGAAGC 59.452 52.381 0.00 0.00 0.00 3.86
268 269 2.826128 TGGTAAGCACTGACTACTGGAG 59.174 50.000 0.00 0.00 0.00 3.86
274 275 6.791867 ATCATAGTTGGTAAGCACTGACTA 57.208 37.500 0.00 0.00 31.43 2.59
277 278 7.791029 TCATAATCATAGTTGGTAAGCACTGA 58.209 34.615 0.00 0.00 0.00 3.41
344 345 3.682155 GCTCAGGAAACATGCTCTCTGAT 60.682 47.826 12.72 0.00 31.93 2.90
349 350 2.290768 ACATGCTCAGGAAACATGCTCT 60.291 45.455 10.31 0.00 43.96 4.09
404 405 4.593206 AGTTGAGACTGACAGGAATGGTTA 59.407 41.667 7.51 0.00 33.99 2.85
417 418 8.558973 AATTAATTCCTTGAGAGTTGAGACTG 57.441 34.615 0.00 0.00 35.88 3.51
457 458 1.216678 ACCACACCCCACAAGATTTCA 59.783 47.619 0.00 0.00 0.00 2.69
498 499 9.323985 GAGTCACAAATCTGAATAATTAGAGCT 57.676 33.333 0.00 0.00 0.00 4.09
499 500 9.323985 AGAGTCACAAATCTGAATAATTAGAGC 57.676 33.333 0.00 0.00 0.00 4.09
501 502 9.823647 GGAGAGTCACAAATCTGAATAATTAGA 57.176 33.333 0.00 0.00 0.00 2.10
502 503 9.829507 AGGAGAGTCACAAATCTGAATAATTAG 57.170 33.333 0.00 0.00 0.00 1.73
504 505 9.171877 GAAGGAGAGTCACAAATCTGAATAATT 57.828 33.333 0.00 0.00 0.00 1.40
505 506 7.772757 GGAAGGAGAGTCACAAATCTGAATAAT 59.227 37.037 0.00 0.00 0.00 1.28
506 507 7.038017 AGGAAGGAGAGTCACAAATCTGAATAA 60.038 37.037 0.00 0.00 0.00 1.40
507 508 6.441924 AGGAAGGAGAGTCACAAATCTGAATA 59.558 38.462 0.00 0.00 0.00 1.75
508 509 5.250313 AGGAAGGAGAGTCACAAATCTGAAT 59.750 40.000 0.00 0.00 0.00 2.57
509 510 4.594920 AGGAAGGAGAGTCACAAATCTGAA 59.405 41.667 0.00 0.00 0.00 3.02
510 511 4.163427 AGGAAGGAGAGTCACAAATCTGA 58.837 43.478 0.00 0.00 0.00 3.27
511 512 4.502962 GAGGAAGGAGAGTCACAAATCTG 58.497 47.826 0.00 0.00 0.00 2.90
512 513 3.517500 GGAGGAAGGAGAGTCACAAATCT 59.482 47.826 0.00 0.00 0.00 2.40
513 514 3.517500 AGGAGGAAGGAGAGTCACAAATC 59.482 47.826 0.00 0.00 0.00 2.17
514 515 3.262915 CAGGAGGAAGGAGAGTCACAAAT 59.737 47.826 0.00 0.00 0.00 2.32
515 516 2.634940 CAGGAGGAAGGAGAGTCACAAA 59.365 50.000 0.00 0.00 0.00 2.83
516 517 2.251818 CAGGAGGAAGGAGAGTCACAA 58.748 52.381 0.00 0.00 0.00 3.33
517 518 1.148027 ACAGGAGGAAGGAGAGTCACA 59.852 52.381 0.00 0.00 0.00 3.58
518 519 1.548269 CACAGGAGGAAGGAGAGTCAC 59.452 57.143 0.00 0.00 0.00 3.67
519 520 1.429299 TCACAGGAGGAAGGAGAGTCA 59.571 52.381 0.00 0.00 0.00 3.41
520 521 2.223803 TCACAGGAGGAAGGAGAGTC 57.776 55.000 0.00 0.00 0.00 3.36
521 522 2.704190 TTCACAGGAGGAAGGAGAGT 57.296 50.000 0.00 0.00 0.00 3.24
522 523 3.071602 TGTTTTCACAGGAGGAAGGAGAG 59.928 47.826 0.00 0.00 0.00 3.20
523 524 3.045634 TGTTTTCACAGGAGGAAGGAGA 58.954 45.455 0.00 0.00 0.00 3.71
524 525 3.492102 TGTTTTCACAGGAGGAAGGAG 57.508 47.619 0.00 0.00 0.00 3.69
525 526 3.138283 ACATGTTTTCACAGGAGGAAGGA 59.862 43.478 0.00 0.00 36.79 3.36
526 527 3.490348 ACATGTTTTCACAGGAGGAAGG 58.510 45.455 0.00 0.00 36.79 3.46
527 528 5.520376 AAACATGTTTTCACAGGAGGAAG 57.480 39.130 18.13 0.00 36.79 3.46
528 529 7.595819 AATAAACATGTTTTCACAGGAGGAA 57.404 32.000 27.66 6.79 36.79 3.36
529 530 8.877864 ATAATAAACATGTTTTCACAGGAGGA 57.122 30.769 27.66 7.30 36.79 3.71
545 546 9.524106 CGGACATGTCAAGTAGTATAATAAACA 57.476 33.333 26.47 0.00 0.00 2.83
546 547 8.975439 CCGGACATGTCAAGTAGTATAATAAAC 58.025 37.037 26.47 2.80 0.00 2.01
547 548 8.698210 ACCGGACATGTCAAGTAGTATAATAAA 58.302 33.333 26.47 0.00 0.00 1.40
548 549 8.241497 ACCGGACATGTCAAGTAGTATAATAA 57.759 34.615 26.47 0.00 0.00 1.40
549 550 7.828508 ACCGGACATGTCAAGTAGTATAATA 57.171 36.000 26.47 0.00 0.00 0.98
550 551 6.726490 ACCGGACATGTCAAGTAGTATAAT 57.274 37.500 26.47 0.00 0.00 1.28
551 552 6.071221 ACAACCGGACATGTCAAGTAGTATAA 60.071 38.462 26.47 0.00 0.00 0.98
552 553 5.419788 ACAACCGGACATGTCAAGTAGTATA 59.580 40.000 26.47 0.00 0.00 1.47
553 554 4.222145 ACAACCGGACATGTCAAGTAGTAT 59.778 41.667 26.47 5.98 0.00 2.12
554 555 3.575256 ACAACCGGACATGTCAAGTAGTA 59.425 43.478 26.47 0.00 0.00 1.82
555 556 2.367567 ACAACCGGACATGTCAAGTAGT 59.632 45.455 26.47 15.66 0.00 2.73
556 557 2.736721 CACAACCGGACATGTCAAGTAG 59.263 50.000 26.47 15.06 0.00 2.57
557 558 2.365941 TCACAACCGGACATGTCAAGTA 59.634 45.455 26.47 5.98 0.00 2.24
558 559 1.140052 TCACAACCGGACATGTCAAGT 59.860 47.619 26.47 19.21 0.00 3.16
559 560 1.877637 TCACAACCGGACATGTCAAG 58.122 50.000 26.47 18.58 0.00 3.02
560 561 2.217750 CTTCACAACCGGACATGTCAA 58.782 47.619 26.47 9.19 0.00 3.18
561 562 1.542328 CCTTCACAACCGGACATGTCA 60.542 52.381 26.47 0.98 0.00 3.58
562 563 1.156736 CCTTCACAACCGGACATGTC 58.843 55.000 17.91 17.91 0.00 3.06
563 564 0.889186 GCCTTCACAACCGGACATGT 60.889 55.000 9.46 7.55 0.00 3.21
564 565 0.888736 TGCCTTCACAACCGGACATG 60.889 55.000 9.46 6.80 0.00 3.21
604 605 4.027674 TCTTGGCAGCATGGTACTTTTA 57.972 40.909 0.00 0.00 35.86 1.52
666 667 4.814771 ACCAAAGTACAACTGTAAGAGTGC 59.185 41.667 0.00 0.00 37.43 4.40
689 690 7.545965 GTGTTCGATCAGAAAAGGAGAAAGATA 59.454 37.037 0.00 0.00 41.10 1.98
696 697 3.433615 GGTGTGTTCGATCAGAAAAGGAG 59.566 47.826 0.00 0.00 41.10 3.69
699 700 4.811555 TTGGTGTGTTCGATCAGAAAAG 57.188 40.909 0.00 0.00 41.10 2.27
707 708 4.080582 TCAGGGATTATTGGTGTGTTCGAT 60.081 41.667 0.00 0.00 0.00 3.59
717 718 7.341769 TGAATTTACTTGGTCAGGGATTATTGG 59.658 37.037 0.00 0.00 0.00 3.16
723 724 5.255397 TGTGAATTTACTTGGTCAGGGAT 57.745 39.130 1.75 0.00 0.00 3.85
727 728 8.567948 AGTAACATTGTGAATTTACTTGGTCAG 58.432 33.333 1.75 0.00 32.06 3.51
773 774 2.256461 GGACAAGCAAAGCTGGCG 59.744 61.111 5.11 0.00 39.62 5.69
852 859 7.487822 TGTATGATTCTTTTCTCTCAGGAGT 57.512 36.000 0.00 0.00 40.29 3.85
856 863 8.123575 CAGCATTGTATGATTCTTTTCTCTCAG 58.876 37.037 0.00 0.00 0.00 3.35
857 864 7.825761 TCAGCATTGTATGATTCTTTTCTCTCA 59.174 33.333 0.00 0.00 0.00 3.27
858 865 8.206325 TCAGCATTGTATGATTCTTTTCTCTC 57.794 34.615 0.00 0.00 0.00 3.20
867 874 5.970023 GTGAGCTTTCAGCATTGTATGATTC 59.030 40.000 0.00 0.00 45.56 2.52
870 877 3.691118 GGTGAGCTTTCAGCATTGTATGA 59.309 43.478 0.00 0.00 45.56 2.15
871 878 3.693085 AGGTGAGCTTTCAGCATTGTATG 59.307 43.478 7.76 0.00 45.56 2.39
942 954 4.083271 GGAGTCCAACAATGTACAGCTTTC 60.083 45.833 3.60 0.00 0.00 2.62
971 983 1.009829 GTAGCAACAGCGGGAGATTG 58.990 55.000 0.00 0.00 0.00 2.67
973 985 0.905357 AAGTAGCAACAGCGGGAGAT 59.095 50.000 0.00 0.00 0.00 2.75
975 987 1.079503 GAAAGTAGCAACAGCGGGAG 58.920 55.000 0.00 0.00 0.00 4.30
979 991 3.878086 TTTCAGAAAGTAGCAACAGCG 57.122 42.857 0.00 0.00 0.00 5.18
1001 1013 3.369681 GCCTGGCAATTCCAAAATGATCA 60.370 43.478 15.17 0.00 46.01 2.92
1025 1037 1.140052 TGAACGTTTCTCCTGCCTTCA 59.860 47.619 0.46 0.00 0.00 3.02
1041 1053 3.194062 GCCTCTTGCTACTGATCTGAAC 58.806 50.000 6.60 0.00 36.87 3.18
1135 1147 3.397482 AGTACAAAGCTGCTTGTCTGAG 58.603 45.455 16.73 4.88 40.08 3.35
1137 1149 3.133691 TGAGTACAAAGCTGCTTGTCTG 58.866 45.455 16.73 12.97 40.08 3.51
1153 1165 8.467598 AGACAATAGAGCGAAACTAAATGAGTA 58.532 33.333 0.00 0.00 37.44 2.59
1154 1166 7.324178 AGACAATAGAGCGAAACTAAATGAGT 58.676 34.615 0.00 0.00 41.56 3.41
1158 1170 9.250624 GATGTAGACAATAGAGCGAAACTAAAT 57.749 33.333 0.00 0.00 0.00 1.40
1167 1179 7.589395 AGTTATGAGATGTAGACAATAGAGCG 58.411 38.462 0.00 0.00 0.00 5.03
1168 1180 8.026607 GGAGTTATGAGATGTAGACAATAGAGC 58.973 40.741 0.00 0.00 0.00 4.09
1231 1243 8.308931 CCAATCAGGTATTCATAAATCCCATTG 58.691 37.037 0.00 0.00 0.00 2.82
1298 1336 6.783892 AATGTGTGTCCAAATTATTTGTGC 57.216 33.333 15.40 8.76 38.98 4.57
1410 1448 6.699575 AAAATATAAGCACCGCTTCATTCT 57.300 33.333 4.16 0.00 46.77 2.40
1503 1541 2.851534 GCAACAAAATGCGACCTAGAC 58.148 47.619 0.00 0.00 36.45 2.59
1525 1563 3.985877 CCAATGGCAACGCAGAGA 58.014 55.556 0.00 0.00 42.51 3.10
1820 1859 4.556697 TGTCCTGATCTTGGAGCCTAATA 58.443 43.478 8.02 0.00 33.78 0.98
1897 1936 5.141910 GAGGGGCAAGAGATTAGTACTAGT 58.858 45.833 0.00 0.00 0.00 2.57
1898 1937 4.525100 GGAGGGGCAAGAGATTAGTACTAG 59.475 50.000 2.23 0.00 0.00 2.57
1899 1938 4.481072 GGAGGGGCAAGAGATTAGTACTA 58.519 47.826 0.00 0.00 0.00 1.82
1900 1939 3.310193 GGAGGGGCAAGAGATTAGTACT 58.690 50.000 0.00 0.00 0.00 2.73
1901 1940 2.036089 CGGAGGGGCAAGAGATTAGTAC 59.964 54.545 0.00 0.00 0.00 2.73
1902 1941 2.317040 CGGAGGGGCAAGAGATTAGTA 58.683 52.381 0.00 0.00 0.00 1.82
2162 2201 7.585579 TGCCAATCATTAGCATAATCTTGAA 57.414 32.000 0.00 0.00 0.00 2.69
2334 2373 2.914734 ATCTTGGATCCCCCGCCTCA 62.915 60.000 9.90 0.00 37.93 3.86
2538 2577 3.317149 ACGGCGACAGCTCTTGTATAATA 59.683 43.478 16.62 0.00 41.05 0.98
2632 2671 1.275291 ACCAATGTTCAGGTCGACGAT 59.725 47.619 9.92 0.00 30.79 3.73
2652 2691 3.731728 GGCCACTGGATGCCCTCA 61.732 66.667 0.00 0.00 41.97 3.86
2747 2786 4.147322 CATGGTGAACGCCGTCGC 62.147 66.667 0.00 0.00 39.84 5.19
2808 2847 3.093057 GAGAGAGCTGTACTGGAAAGGA 58.907 50.000 0.00 0.00 0.00 3.36
2811 2850 3.501349 ACAGAGAGAGCTGTACTGGAAA 58.499 45.455 17.37 0.00 46.67 3.13
2890 2929 1.802960 GCCTGTTGTGTCACATGAGAG 59.197 52.381 6.48 0.66 0.00 3.20
2898 2937 1.151221 AGGCATGCCTGTTGTGTCA 59.849 52.632 38.23 0.00 46.22 3.58
2908 2947 0.890683 AGCAACTTGTAAGGCATGCC 59.109 50.000 30.12 30.12 35.91 4.40
3013 3052 1.153804 GAGACGCCTCCTTTCCGAC 60.154 63.158 0.00 0.00 33.30 4.79
3223 3262 2.024369 ACCTTTCCAAAACCACAGGAGT 60.024 45.455 0.00 0.00 32.11 3.85
3229 3268 2.565391 CCCCATACCTTTCCAAAACCAC 59.435 50.000 0.00 0.00 0.00 4.16
3230 3269 2.896039 CCCCATACCTTTCCAAAACCA 58.104 47.619 0.00 0.00 0.00 3.67
3411 3450 6.017109 ACACAAATAAAGAACGTCATGAGCTT 60.017 34.615 0.00 0.00 0.00 3.74
3433 3472 2.108700 CTGCAACGCTTACAACAACAC 58.891 47.619 0.00 0.00 0.00 3.32
3502 3541 4.405358 AGAGAGAAAGGCTGAGATCGAAAT 59.595 41.667 0.00 0.00 0.00 2.17
3507 3546 3.118665 AGCAAGAGAGAAAGGCTGAGATC 60.119 47.826 0.00 0.00 32.76 2.75
3678 3834 0.179056 ACTGGTTGACACCTGGTTCG 60.179 55.000 0.00 0.00 44.56 3.95
3838 3994 3.018856 CTCTATTTTGTGCAGATGGGCA 58.981 45.455 0.00 0.00 42.53 5.36
3985 4141 3.755905 TCATGAATACGGCTGCAGAAAAA 59.244 39.130 20.43 0.00 0.00 1.94
4225 4381 1.800586 GCGACTGCTGAAATCAGAACA 59.199 47.619 14.43 3.00 46.59 3.18
4334 4490 2.037902 TGTGGATCCTTAGCAACACGAA 59.962 45.455 14.23 0.00 0.00 3.85
4355 4511 2.486191 CCTCTGCTTCCTCAACAACAGT 60.486 50.000 0.00 0.00 0.00 3.55
4379 4535 2.777094 TCTTCGATTTGTGATGTGCCA 58.223 42.857 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.