Multiple sequence alignment - TraesCS5A01G186200

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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 TraesCS5A01G186200 chr5A 100.000 3410 0 0 1 3410 386696964 386700373 0.000000e+00 6298.0
1 TraesCS5A01G186200 chr5A 79.532 171 25 7 221 383 575713416 575713584 2.780000e-21 113.0
2 TraesCS5A01G186200 chr5A 89.157 83 6 3 221 302 575714295 575714375 2.170000e-17 100.0
3 TraesCS5A01G186200 chr5B 92.258 2932 169 36 3 2917 335200641 335203531 0.000000e+00 4104.0
4 TraesCS5A01G186200 chr5B 90.820 512 24 5 2911 3410 335203561 335204061 0.000000e+00 664.0
5 TraesCS5A01G186200 chr5B 80.829 193 35 2 7 198 586848114 586848305 2.120000e-32 150.0
6 TraesCS5A01G186200 chr5D 96.349 2191 61 11 733 2917 293656767 293658944 0.000000e+00 3585.0
7 TraesCS5A01G186200 chr5D 88.594 640 60 10 1 630 293654855 293655491 0.000000e+00 765.0
8 TraesCS5A01G186200 chr5D 95.299 234 5 2 3177 3410 293659205 293659432 1.930000e-97 366.0
9 TraesCS5A01G186200 chr5D 95.477 199 7 1 2911 3109 293658974 293659170 1.970000e-82 316.0
10 TraesCS5A01G186200 chr5D 83.523 176 24 5 495 667 251938127 251937954 3.520000e-35 159.0
11 TraesCS5A01G186200 chr7B 79.803 203 39 2 2 203 621296011 621296212 2.740000e-31 147.0
12 TraesCS5A01G186200 chr2D 83.871 155 22 3 519 671 61795779 61795932 9.860000e-31 145.0
13 TraesCS5A01G186200 chr2D 96.970 33 1 0 432 464 95289998 95290030 4.750000e-04 56.5
14 TraesCS5A01G186200 chr4A 85.470 117 13 4 523 637 134070916 134070802 5.980000e-23 119.0
15 TraesCS5A01G186200 chr3A 76.804 194 43 2 20 213 654208529 654208720 1.290000e-19 108.0
16 TraesCS5A01G186200 chr3A 89.157 83 9 0 221 303 12182192 12182110 1.670000e-18 104.0
17 TraesCS5A01G186200 chr3A 77.401 177 38 2 1 176 623602034 623602209 1.670000e-18 104.0
18 TraesCS5A01G186200 chr3A 97.297 37 1 0 384 420 603211052 603211088 2.840000e-06 63.9
19 TraesCS5A01G186200 chr6D 80.833 120 23 0 7 126 413321961 413322080 1.010000e-15 95.3
20 TraesCS5A01G186200 chr1D 76.142 197 36 9 1 191 437902946 437903137 3.620000e-15 93.5
21 TraesCS5A01G186200 chr1B 75.269 186 35 9 4 184 593495153 593495332 1.010000e-10 78.7
22 TraesCS5A01G186200 chr7A 95.652 46 2 0 219 264 486149686 486149641 1.310000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G186200 chr5A 386696964 386700373 3409 False 6298 6298 100.00000 1 3410 1 chr5A.!!$F1 3409
1 TraesCS5A01G186200 chr5B 335200641 335204061 3420 False 2384 4104 91.53900 3 3410 2 chr5B.!!$F2 3407
2 TraesCS5A01G186200 chr5D 293654855 293659432 4577 False 1258 3585 93.92975 1 3410 4 chr5D.!!$F1 3409

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
737 1199 0.036388 GGTCCACCTTTGAGATGCGA 60.036 55.000 0.0 0.0 0.0 5.10 F
892 2091 1.073098 ACCCTCCCTAACAAACCTGG 58.927 55.000 0.0 0.0 0.0 4.45 F
1562 2763 1.074775 GCCACCACCAGATCACCAA 59.925 57.895 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 3556 0.318441 TCTTCGGAACAGCTCCAGTG 59.682 55.000 0.0 0.0 45.74 3.66 R
2366 3567 1.555075 CCCAGACCAGATTCTTCGGAA 59.445 52.381 0.0 0.0 38.42 4.30 R
3129 4371 0.521735 CTGTAGCCTCCGTTTTTGCC 59.478 55.000 0.0 0.0 0.00 4.52 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
86 87 0.657840 GCCGACCATGAGTACAATGC 59.342 55.000 0.00 0.00 0.00 3.56
107 108 2.046892 CCTCCCTGACAAGCACCG 60.047 66.667 0.00 0.00 0.00 4.94
121 122 3.449227 ACCGATGCGCGAAGGAGA 61.449 61.111 12.10 0.00 44.57 3.71
134 135 3.387947 GGAGAAACTCCCCGCCGA 61.388 66.667 6.54 0.00 44.36 5.54
213 214 0.970427 ACACCGCCCATGAAAATCCC 60.970 55.000 0.00 0.00 0.00 3.85
266 268 1.115930 AGGCGGCGGATGAAGTCTAT 61.116 55.000 9.78 0.00 0.00 1.98
305 307 4.838486 GACGTCGCCTGCTCCTCG 62.838 72.222 0.00 0.00 0.00 4.63
372 375 3.474798 TGACAGTGGGGAAGAGTAGAT 57.525 47.619 0.00 0.00 0.00 1.98
420 423 0.098200 TCGTCAGCCGATTAGACACG 59.902 55.000 0.00 0.00 41.60 4.49
430 433 1.204941 GATTAGACACGGGCAGACTGT 59.795 52.381 3.99 0.00 40.00 3.55
435 438 2.031163 ACGGGCAGACTGTGAAGC 59.969 61.111 3.99 0.00 37.28 3.86
464 467 1.666209 ATTTTTCGGGGCTCATGGCG 61.666 55.000 0.00 0.00 42.94 5.69
465 468 3.561120 TTTTCGGGGCTCATGGCGT 62.561 57.895 0.00 0.00 42.94 5.68
468 471 4.776322 CGGGGCTCATGGCGTGAA 62.776 66.667 11.12 0.00 42.94 3.18
469 472 2.124151 GGGGCTCATGGCGTGAAT 60.124 61.111 11.12 0.00 42.94 2.57
470 473 1.754234 GGGGCTCATGGCGTGAATT 60.754 57.895 11.12 0.00 42.94 2.17
471 474 1.322538 GGGGCTCATGGCGTGAATTT 61.323 55.000 11.12 0.00 42.94 1.82
472 475 1.388547 GGGCTCATGGCGTGAATTTA 58.611 50.000 11.12 0.00 42.94 1.40
473 476 1.334869 GGGCTCATGGCGTGAATTTAG 59.665 52.381 11.12 0.00 42.94 1.85
474 477 1.268743 GGCTCATGGCGTGAATTTAGC 60.269 52.381 11.12 9.83 42.94 3.09
475 478 1.672881 GCTCATGGCGTGAATTTAGCT 59.327 47.619 11.12 0.00 36.14 3.32
619 628 6.616774 ACCGCATCAAATTTGTTCAATTTT 57.383 29.167 17.47 1.29 41.57 1.82
667 707 5.295787 CGGACATATGTGGCTAGCTTTAAAA 59.704 40.000 14.43 0.00 32.35 1.52
679 719 1.402852 GCTTTAAAAGGCCAGCTTCCG 60.403 52.381 5.01 0.00 0.00 4.30
684 724 0.462047 AAAGGCCAGCTTCCGTATCG 60.462 55.000 5.01 0.00 0.00 2.92
689 729 1.278238 CCAGCTTCCGTATCGTTGTC 58.722 55.000 0.00 0.00 0.00 3.18
690 730 1.135083 CCAGCTTCCGTATCGTTGTCT 60.135 52.381 0.00 0.00 0.00 3.41
696 736 2.097036 TCCGTATCGTTGTCTGTGGAT 58.903 47.619 0.00 0.00 0.00 3.41
697 737 3.281158 TCCGTATCGTTGTCTGTGGATA 58.719 45.455 0.00 0.00 0.00 2.59
698 738 3.314357 TCCGTATCGTTGTCTGTGGATAG 59.686 47.826 0.00 0.00 0.00 2.08
699 739 3.314357 CCGTATCGTTGTCTGTGGATAGA 59.686 47.826 0.00 0.00 0.00 1.98
700 740 4.023107 CCGTATCGTTGTCTGTGGATAGAT 60.023 45.833 0.00 0.00 0.00 1.98
701 741 4.912187 CGTATCGTTGTCTGTGGATAGATG 59.088 45.833 0.00 0.00 0.00 2.90
702 742 3.165058 TCGTTGTCTGTGGATAGATGC 57.835 47.619 0.00 0.00 0.00 3.91
703 743 1.854743 CGTTGTCTGTGGATAGATGCG 59.145 52.381 0.00 0.00 0.00 4.73
704 744 2.205074 GTTGTCTGTGGATAGATGCGG 58.795 52.381 0.00 0.00 0.00 5.69
705 745 1.485124 TGTCTGTGGATAGATGCGGT 58.515 50.000 0.00 0.00 0.00 5.68
706 746 1.136891 TGTCTGTGGATAGATGCGGTG 59.863 52.381 0.00 0.00 0.00 4.94
707 747 0.104855 TCTGTGGATAGATGCGGTGC 59.895 55.000 0.00 0.00 0.00 5.01
728 768 1.152138 GGTTTCCGGGTCCACCTTT 59.848 57.895 0.00 0.00 36.97 3.11
729 769 1.176619 GGTTTCCGGGTCCACCTTTG 61.177 60.000 0.00 0.00 36.97 2.77
730 770 0.179012 GTTTCCGGGTCCACCTTTGA 60.179 55.000 0.00 0.00 36.97 2.69
731 771 0.109723 TTTCCGGGTCCACCTTTGAG 59.890 55.000 0.00 0.00 36.97 3.02
733 1195 0.546747 TCCGGGTCCACCTTTGAGAT 60.547 55.000 0.00 0.00 36.97 2.75
735 1197 1.026718 CGGGTCCACCTTTGAGATGC 61.027 60.000 0.00 0.00 36.97 3.91
737 1199 0.036388 GGTCCACCTTTGAGATGCGA 60.036 55.000 0.00 0.00 0.00 5.10
790 1985 4.514441 CGCTCAGCCAATTTCAGATTATCT 59.486 41.667 0.00 0.00 0.00 1.98
891 2090 1.271926 CCACCCTCCCTAACAAACCTG 60.272 57.143 0.00 0.00 0.00 4.00
892 2091 1.073098 ACCCTCCCTAACAAACCTGG 58.927 55.000 0.00 0.00 0.00 4.45
893 2092 1.368374 CCCTCCCTAACAAACCTGGA 58.632 55.000 0.00 0.00 0.00 3.86
894 2093 1.708551 CCCTCCCTAACAAACCTGGAA 59.291 52.381 0.00 0.00 0.00 3.53
926 2125 4.689612 TTTAAGATCCGATCTCCCCTTG 57.310 45.455 11.40 0.00 39.08 3.61
1554 2755 4.394712 GACTCCGGCCACCACCAG 62.395 72.222 2.24 0.00 0.00 4.00
1562 2763 1.074775 GCCACCACCAGATCACCAA 59.925 57.895 0.00 0.00 0.00 3.67
1599 2800 2.922162 CCTCCTGCAGGTGGTATCT 58.078 57.895 35.88 0.00 42.41 1.98
1857 3058 7.353525 TGGGATTTGCAAGGATAAATCTTCTA 58.646 34.615 0.00 0.00 41.04 2.10
1929 3130 2.586357 GAGATCGCCGGAGTTGCC 60.586 66.667 5.05 0.00 0.00 4.52
2169 3370 2.557452 GGATTGGTTCCATGGTGGTCTT 60.557 50.000 12.58 0.00 44.74 3.01
2211 3412 4.082523 TTTCCTCGCCTGCCTCGG 62.083 66.667 0.00 0.00 0.00 4.63
2220 3421 2.125512 CTGCCTCGGTGCCACTAC 60.126 66.667 0.00 0.00 0.00 2.73
2298 3499 2.440980 GCCACATTCTGGGAGGCC 60.441 66.667 0.00 0.00 41.02 5.19
2366 3567 2.403132 GAAGCCACCACTGGAGCTGT 62.403 60.000 15.35 8.04 40.55 4.40
2491 3693 2.976589 TCTGATTGCTTCTCGATTGCA 58.023 42.857 3.53 3.53 34.69 4.08
2498 3700 3.974912 TGCTTCTCGATTGCATAGAGAG 58.025 45.455 13.50 8.77 41.10 3.20
2514 3716 6.371271 GCATAGAGAGATTGATCCTTTTAGCC 59.629 42.308 0.00 0.00 0.00 3.93
2521 3723 2.985896 TGATCCTTTTAGCCGTTGGAG 58.014 47.619 0.00 0.00 0.00 3.86
2530 3732 1.593209 GCCGTTGGAGTCGTGTTGA 60.593 57.895 0.00 0.00 0.00 3.18
2547 3749 4.092091 GTGTTGAATTTTTCGTGTTGCCAA 59.908 37.500 0.00 0.00 0.00 4.52
2566 3768 4.614535 GCCAAGTGACTATCTTTGCAGTTG 60.615 45.833 0.00 0.00 39.92 3.16
2622 3824 5.852282 ACACCATATTTAGATTGTTGGGC 57.148 39.130 0.00 0.00 0.00 5.36
2624 3826 6.668645 ACACCATATTTAGATTGTTGGGCTA 58.331 36.000 0.00 0.00 0.00 3.93
2643 3845 4.954826 GGCTATCCCTATCACGGTAACTAT 59.045 45.833 0.00 0.00 0.00 2.12
2649 3851 7.458409 TCCCTATCACGGTAACTATATCAAC 57.542 40.000 0.00 0.00 0.00 3.18
2743 3947 7.920151 TGAAACTGTAAACTCAATTGATGGTTG 59.080 33.333 8.96 0.00 0.00 3.77
2749 3953 3.356290 ACTCAATTGATGGTTGGTAGCC 58.644 45.455 8.96 0.00 0.00 3.93
2758 3964 4.021456 TGATGGTTGGTAGCCTGTATATCG 60.021 45.833 0.00 0.00 0.00 2.92
2767 3973 2.029828 AGCCTGTATATCGTGCTGCTAC 60.030 50.000 0.00 0.00 0.00 3.58
2815 4021 7.860872 GGAACATGACGATTCCAATAATAAACC 59.139 37.037 0.00 0.00 43.40 3.27
2821 4027 8.617809 TGACGATTCCAATAATAAACCTTTAGC 58.382 33.333 0.00 0.00 0.00 3.09
2851 4057 5.521906 TTCTACTGCATCTGTATGTCCTC 57.478 43.478 0.00 0.00 35.38 3.71
2860 4067 4.220693 TCTGTATGTCCTCCATGGTTTG 57.779 45.455 12.58 3.46 34.86 2.93
3000 4242 4.897025 AGCTTTCAGATTTATGAGCAGC 57.103 40.909 0.00 0.00 37.49 5.25
3051 4293 3.242870 GCTGGATTCGCCTAACAATTCAG 60.243 47.826 0.00 0.00 38.29 3.02
3109 4351 7.412137 TCTGCATATCATAAGTTCACAATCG 57.588 36.000 0.00 0.00 0.00 3.34
3129 4371 4.122046 TCGGTAGCATCATTTGTCTCATG 58.878 43.478 0.00 0.00 0.00 3.07
3136 4378 4.691685 GCATCATTTGTCTCATGGCAAAAA 59.308 37.500 12.44 0.47 37.98 1.94
3142 4384 1.200020 GTCTCATGGCAAAAACGGAGG 59.800 52.381 0.00 0.00 0.00 4.30
3147 4389 0.179015 TGGCAAAAACGGAGGCTACA 60.179 50.000 0.00 0.00 0.00 2.74
3148 4390 0.521735 GGCAAAAACGGAGGCTACAG 59.478 55.000 0.00 0.00 0.00 2.74
3149 4391 1.235724 GCAAAAACGGAGGCTACAGT 58.764 50.000 0.00 0.00 0.00 3.55
3150 4392 1.607148 GCAAAAACGGAGGCTACAGTT 59.393 47.619 0.00 0.00 0.00 3.16
3191 4445 5.278022 GCATAACTGACTAGGGCTAATTTGC 60.278 44.000 3.03 3.03 0.00 3.68
3209 4463 4.640771 TTGCCAAGTCCTAGACAATTCT 57.359 40.909 0.00 0.00 34.60 2.40
3384 4638 1.068474 CGATTCGTCACTGGTGGTTC 58.932 55.000 0.00 0.00 0.00 3.62
3386 4640 0.391597 ATTCGTCACTGGTGGTTCGT 59.608 50.000 0.70 0.00 0.00 3.85
3387 4641 1.031235 TTCGTCACTGGTGGTTCGTA 58.969 50.000 0.70 0.00 0.00 3.43
3388 4642 0.594602 TCGTCACTGGTGGTTCGTAG 59.405 55.000 0.70 0.00 0.00 3.51
3389 4643 0.313043 CGTCACTGGTGGTTCGTAGT 59.687 55.000 0.70 0.00 0.00 2.73
3390 4644 1.536766 CGTCACTGGTGGTTCGTAGTA 59.463 52.381 0.70 0.00 0.00 1.82
3391 4645 2.666619 CGTCACTGGTGGTTCGTAGTAC 60.667 54.545 0.70 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 4.785453 GCTTGTCAGGGAGGCGGG 62.785 72.222 0.00 0.00 0.00 6.13
107 108 0.647925 GAGTTTCTCCTTCGCGCATC 59.352 55.000 8.75 0.00 0.00 3.91
121 122 4.157120 CGGATCGGCGGGGAGTTT 62.157 66.667 7.21 0.00 0.00 2.66
127 128 4.664677 GATGGTCGGATCGGCGGG 62.665 72.222 7.21 0.00 29.52 6.13
266 268 1.186200 CCTCGTCCTCATCCTTGTCA 58.814 55.000 0.00 0.00 0.00 3.58
305 307 3.248171 GTCATGCCGACGAGCGTC 61.248 66.667 12.65 12.65 41.40 5.19
345 348 1.678598 TTCCCCACTGTCAACGACGT 61.679 55.000 0.00 0.00 34.95 4.34
372 375 0.911769 CACCAAGCTACCTCCCATGA 59.088 55.000 0.00 0.00 0.00 3.07
416 419 1.069765 CTTCACAGTCTGCCCGTGT 59.930 57.895 0.00 0.00 32.42 4.49
418 421 2.031163 GCTTCACAGTCTGCCCGT 59.969 61.111 0.00 0.00 0.00 5.28
420 423 2.743928 CGGCTTCACAGTCTGCCC 60.744 66.667 0.00 0.00 42.15 5.36
435 438 0.109319 CCCGAAAAATGAAGCACCGG 60.109 55.000 0.00 0.00 35.68 5.28
464 467 2.742053 TCAACGCTCCAGCTAAATTCAC 59.258 45.455 0.00 0.00 39.32 3.18
465 468 2.742053 GTCAACGCTCCAGCTAAATTCA 59.258 45.455 0.00 0.00 39.32 2.57
467 470 1.732259 CGTCAACGCTCCAGCTAAATT 59.268 47.619 0.00 0.00 39.32 1.82
468 471 1.359848 CGTCAACGCTCCAGCTAAAT 58.640 50.000 0.00 0.00 39.32 1.40
469 472 0.669318 CCGTCAACGCTCCAGCTAAA 60.669 55.000 0.00 0.00 39.32 1.85
470 473 1.080093 CCGTCAACGCTCCAGCTAA 60.080 57.895 0.00 0.00 39.32 3.09
471 474 0.961857 TACCGTCAACGCTCCAGCTA 60.962 55.000 0.00 0.00 39.32 3.32
472 475 1.812686 TTACCGTCAACGCTCCAGCT 61.813 55.000 0.00 0.00 39.32 4.24
473 476 0.739813 ATTACCGTCAACGCTCCAGC 60.740 55.000 0.00 0.00 38.18 4.85
474 477 1.722011 AATTACCGTCAACGCTCCAG 58.278 50.000 0.00 0.00 38.18 3.86
475 478 2.172851 AAATTACCGTCAACGCTCCA 57.827 45.000 0.00 0.00 38.18 3.86
482 490 9.643693 CTAAACCTAGACTAAAATTACCGTCAA 57.356 33.333 0.00 0.00 0.00 3.18
483 491 9.023962 TCTAAACCTAGACTAAAATTACCGTCA 57.976 33.333 0.00 0.00 0.00 4.35
498 506 7.687388 TGAACTAGAGTGACTCTAAACCTAGA 58.313 38.462 21.50 0.83 41.74 2.43
578 587 7.388224 TGATGCGGTATTTAAACAAACTAGACA 59.612 33.333 0.00 0.00 0.00 3.41
582 591 9.915629 AATTTGATGCGGTATTTAAACAAACTA 57.084 25.926 0.00 0.00 0.00 2.24
583 592 8.825667 AATTTGATGCGGTATTTAAACAAACT 57.174 26.923 0.00 0.00 0.00 2.66
585 594 9.046296 ACAAATTTGATGCGGTATTTAAACAAA 57.954 25.926 24.64 0.00 0.00 2.83
619 628 8.115520 CCGTTTGTATTCGGTCGAAATTTAATA 58.884 33.333 9.88 0.00 41.58 0.98
638 678 2.489938 AGCCACATATGTCCGTTTGT 57.510 45.000 5.07 0.00 0.00 2.83
642 682 1.414158 AGCTAGCCACATATGTCCGT 58.586 50.000 12.13 0.00 0.00 4.69
650 690 2.760650 GGCCTTTTAAAGCTAGCCACAT 59.239 45.455 12.13 0.00 40.20 3.21
667 707 1.614241 AACGATACGGAAGCTGGCCT 61.614 55.000 3.32 0.00 0.00 5.19
679 719 4.681942 GCATCTATCCACAGACAACGATAC 59.318 45.833 0.00 0.00 0.00 2.24
684 724 2.205074 CCGCATCTATCCACAGACAAC 58.795 52.381 0.00 0.00 0.00 3.32
689 729 0.882042 GGCACCGCATCTATCCACAG 60.882 60.000 0.00 0.00 0.00 3.66
690 730 1.146041 GGCACCGCATCTATCCACA 59.854 57.895 0.00 0.00 0.00 4.17
711 751 0.179012 TCAAAGGTGGACCCGGAAAC 60.179 55.000 0.73 0.00 38.74 2.78
716 756 1.026718 GCATCTCAAAGGTGGACCCG 61.027 60.000 0.00 0.00 38.74 5.28
723 763 1.139853 GGATCCTCGCATCTCAAAGGT 59.860 52.381 3.84 0.00 0.00 3.50
728 768 0.540597 ATCCGGATCCTCGCATCTCA 60.541 55.000 12.38 0.00 0.00 3.27
729 769 0.172352 GATCCGGATCCTCGCATCTC 59.828 60.000 30.80 5.88 31.76 2.75
730 770 2.271940 GATCCGGATCCTCGCATCT 58.728 57.895 30.80 0.00 31.76 2.90
731 771 4.900154 GATCCGGATCCTCGCATC 57.100 61.111 30.80 7.45 31.76 3.91
790 1985 1.337447 CCTCTTCGCTCCACGGTAAAA 60.337 52.381 0.00 0.00 43.89 1.52
893 2092 9.626831 AGATCGGATCTTAAAACAGGAACGGTT 62.627 40.741 14.68 0.00 42.46 4.44
894 2093 3.007182 TCGGATCTTAAAACAGGAACGGT 59.993 43.478 0.00 0.00 39.31 4.83
936 2135 3.711782 AAGGGAGGGGAGGGGAGG 61.712 72.222 0.00 0.00 0.00 4.30
937 2136 2.040359 GAAGGGAGGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
938 2137 3.707189 GGAAGGGAGGGGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
939 2138 3.711782 AGGAAGGGAGGGGAGGGG 61.712 72.222 0.00 0.00 0.00 4.79
940 2139 2.040359 GAGGAAGGGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
1071 2272 4.891727 ATCATGCGGACGTCGGCC 62.892 66.667 35.71 22.37 40.88 6.13
1554 2755 2.401766 CGCAGGGTGCTTGGTGATC 61.402 63.158 0.00 0.00 42.25 2.92
1596 2797 1.903877 CGGTGAGGCAGTTCCCAGAT 61.904 60.000 0.00 0.00 34.51 2.90
1599 2800 3.636231 CCGGTGAGGCAGTTCCCA 61.636 66.667 0.00 0.00 34.51 4.37
1857 3058 1.070758 AGGAACACGATTGACTGCACT 59.929 47.619 0.00 0.00 0.00 4.40
1929 3130 1.571215 GGTACCAAACCCAGAACGCG 61.571 60.000 7.15 3.53 43.16 6.01
2169 3370 2.341846 GGTGTTCAACCTGGAACTGA 57.658 50.000 0.00 0.00 46.55 3.41
2211 3412 0.460284 CGACCATCCTGTAGTGGCAC 60.460 60.000 10.29 10.29 39.13 5.01
2220 3421 4.592192 ATCGGCGCGACCATCCTG 62.592 66.667 12.10 0.00 39.18 3.86
2298 3499 4.333649 AGCGTCTTCCATGTCATTACATTG 59.666 41.667 0.00 0.00 44.07 2.82
2355 3556 0.318441 TCTTCGGAACAGCTCCAGTG 59.682 55.000 0.00 0.00 45.74 3.66
2366 3567 1.555075 CCCAGACCAGATTCTTCGGAA 59.445 52.381 0.00 0.00 38.42 4.30
2467 3669 5.761726 TGCAATCGAGAAGCAATCAGATAAT 59.238 36.000 6.73 0.00 34.97 1.28
2491 3693 6.268847 ACGGCTAAAAGGATCAATCTCTCTAT 59.731 38.462 0.00 0.00 0.00 1.98
2498 3700 3.945285 TCCAACGGCTAAAAGGATCAATC 59.055 43.478 0.00 0.00 0.00 2.67
2514 3716 3.602390 AAATTCAACACGACTCCAACG 57.398 42.857 0.00 0.00 0.00 4.10
2521 3723 4.545519 GCAACACGAAAAATTCAACACGAC 60.546 41.667 0.00 0.00 0.00 4.34
2547 3749 5.349817 CGATTCAACTGCAAAGATAGTCACT 59.650 40.000 0.00 0.00 0.00 3.41
2566 3768 2.083774 TGAAGCATGAACCCACGATTC 58.916 47.619 0.00 0.00 0.00 2.52
2622 3824 8.975663 TGATATAGTTACCGTGATAGGGATAG 57.024 38.462 0.00 0.00 35.02 2.08
2624 3826 7.672660 TGTTGATATAGTTACCGTGATAGGGAT 59.327 37.037 0.00 0.00 35.02 3.85
2634 3836 9.745880 AATCAAGTACTGTTGATATAGTTACCG 57.254 33.333 9.89 0.00 44.72 4.02
2743 3947 2.927014 GCAGCACGATATACAGGCTACC 60.927 54.545 0.00 0.00 32.71 3.18
2749 3953 2.585845 CCGTAGCAGCACGATATACAG 58.414 52.381 16.05 0.00 44.69 2.74
2787 3993 2.122783 TTGGAATCGTCATGTTCCCC 57.877 50.000 9.63 0.00 42.56 4.81
2828 4034 5.163405 GGAGGACATACAGATGCAGTAGAAA 60.163 44.000 0.00 0.00 36.43 2.52
2829 4035 4.342378 GGAGGACATACAGATGCAGTAGAA 59.658 45.833 0.00 0.00 36.43 2.10
2830 4036 3.891977 GGAGGACATACAGATGCAGTAGA 59.108 47.826 0.00 0.00 36.43 2.59
2840 4046 4.220693 TCAAACCATGGAGGACATACAG 57.779 45.455 21.47 0.00 41.22 2.74
3000 4242 4.022762 AGTCTCTAGGCAGCATATAACACG 60.023 45.833 0.00 0.00 0.00 4.49
3051 4293 7.775561 ACAAGACCAATGGATAGTATCTTTTCC 59.224 37.037 6.16 0.00 0.00 3.13
3109 4351 3.004106 GCCATGAGACAAATGATGCTACC 59.996 47.826 0.00 0.00 0.00 3.18
3129 4371 0.521735 CTGTAGCCTCCGTTTTTGCC 59.478 55.000 0.00 0.00 0.00 4.52
3136 4378 0.537188 CATGGAACTGTAGCCTCCGT 59.463 55.000 1.99 0.00 31.37 4.69
3147 4389 3.077359 GCAAGAACAGTAGCATGGAACT 58.923 45.455 0.00 0.00 0.00 3.01
3148 4390 2.813754 TGCAAGAACAGTAGCATGGAAC 59.186 45.455 0.00 0.00 31.05 3.62
3149 4391 3.138884 TGCAAGAACAGTAGCATGGAA 57.861 42.857 0.00 0.00 31.05 3.53
3150 4392 2.857186 TGCAAGAACAGTAGCATGGA 57.143 45.000 0.00 0.00 31.05 3.41
3191 4445 5.165961 TCCAAGAATTGTCTAGGACTTGG 57.834 43.478 14.94 14.94 46.99 3.61
3198 4452 8.200120 TGTAGATCACATCCAAGAATTGTCTAG 58.800 37.037 0.00 0.00 36.89 2.43
3236 4490 0.667993 CACGATGCCAGTTGTTTGGT 59.332 50.000 0.00 0.00 40.49 3.67
3384 4638 0.924363 CGCTGCACGCTAGTACTACG 60.924 60.000 17.61 17.61 36.13 3.51


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

AutoCloner maintained by Alex Coulton.