Multiple sequence alignment - TraesCS7D01G240900

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 TraesCS7D01G240900 chr7D 100.000 3692 0 0 1 3692 205495842 205499533 0.000000e+00 6818.0
1 TraesCS7D01G240900 chr7A 96.002 3402 106 14 13 3396 217528294 217531683 0.000000e+00 5502.0
2 TraesCS7D01G240900 chr7A 90.226 133 12 1 3394 3526 217548892 217549023 4.900000e-39 172.0
3 TraesCS7D01G240900 chr7B 96.683 2442 72 4 689 3123 197001024 196998585 0.000000e+00 4052.0
4 TraesCS7D01G240900 chr7B 91.690 710 40 9 3 706 197003428 197002732 0.000000e+00 966.0
5 TraesCS7D01G240900 chr7B 92.941 425 22 2 3121 3545 196998427 196998011 2.440000e-171 612.0
6 TraesCS7D01G240900 chr4A 82.320 181 27 3 3515 3691 252667423 252667244 6.390000e-33 152.0
7 TraesCS7D01G240900 chr4A 85.047 107 11 4 3515 3617 465796838 465796943 1.810000e-18 104.0
8 TraesCS7D01G240900 chr2B 81.667 180 21 8 3516 3685 23004508 23004685 4.970000e-29 139.0
9 TraesCS7D01G240900 chr2B 79.781 183 26 9 3516 3689 209817067 209816887 5.010000e-24 122.0
10 TraesCS7D01G240900 chr2A 80.220 182 29 6 3518 3692 763476019 763475838 2.990000e-26 130.0
11 TraesCS7D01G240900 chr4D 85.841 113 13 2 3552 3661 363573743 363573855 2.330000e-22 117.0
12 TraesCS7D01G240900 chr4D 82.400 125 16 5 3518 3637 111136628 111136505 1.810000e-18 104.0
13 TraesCS7D01G240900 chrUn 84.211 114 13 3 3581 3690 294976852 294976964 5.040000e-19 106.0
14 TraesCS7D01G240900 chrUn 84.211 114 13 3 3581 3690 301544038 301544150 5.040000e-19 106.0
15 TraesCS7D01G240900 chr3D 76.744 172 30 9 3518 3683 58599289 58599122 1.830000e-13 87.9


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 TraesCS7D01G240900 chr7D 205495842 205499533 3691 False 6818.000000 6818 100.000000 1 3692 1 chr7D.!!$F1 3691
1 TraesCS7D01G240900 chr7A 217528294 217531683 3389 False 5502.000000 5502 96.002000 13 3396 1 chr7A.!!$F1 3383
2 TraesCS7D01G240900 chr7B 196998011 197003428 5417 True 1876.666667 4052 93.771333 3 3545 3 chr7B.!!$R1 3542

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
442 451 0.538287 AGGCTTCAGTTTGTGCTCCC 60.538 55.0 0.00 0.0 0.00 4.30 F
1432 3172 0.034896 TCCAGAAGTTTCTCGGGCAC 59.965 55.0 9.14 0.0 34.74 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 3578 1.801025 GCACGACTTTTGGTGGTTTGG 60.801 52.381 0.00 0.0 34.69 3.28 R
2788 4531 0.454452 GCCAATTCGACTTCGCAACC 60.454 55.000 0.35 0.0 39.60 3.77 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
85 86 3.083349 CCAGTCCATCTCGCCCCA 61.083 66.667 0.00 0.00 0.00 4.96
86 87 2.669133 CCAGTCCATCTCGCCCCAA 61.669 63.158 0.00 0.00 0.00 4.12
126 127 3.090532 CCTTTCCCCTCCCCTCCG 61.091 72.222 0.00 0.00 0.00 4.63
351 360 6.654582 TGAGCTTCAGTTATTGCTAATTGTGA 59.345 34.615 0.00 0.00 35.76 3.58
423 432 2.432456 GGTGCATGCGTGTCTCGA 60.432 61.111 14.09 0.00 42.86 4.04
442 451 0.538287 AGGCTTCAGTTTGTGCTCCC 60.538 55.000 0.00 0.00 0.00 4.30
487 496 2.963782 TCTAGGAGGTCCGAATTTAGGC 59.036 50.000 0.00 0.00 42.08 3.93
524 534 2.741486 TTCGCTGGTGGGGTTAGTGC 62.741 60.000 0.00 0.00 0.00 4.40
588 598 7.552687 TGATTGTATAAGTTAGGCCAACAGAAG 59.447 37.037 5.01 0.00 39.81 2.85
647 661 2.432874 GGAAGAGAAGGGCTAGAAGGAC 59.567 54.545 0.00 0.00 0.00 3.85
687 701 2.993899 GTTCATACTTCTGGACCGTGTG 59.006 50.000 0.00 0.00 0.00 3.82
842 2582 8.698973 TTTCCAAGTTGAACTATTGGTGAATA 57.301 30.769 13.98 0.00 43.28 1.75
849 2589 7.673926 AGTTGAACTATTGGTGAATATTGGGTT 59.326 33.333 0.00 0.00 0.00 4.11
877 2617 4.249661 TCGCTGATATGTGCTTGTTTACA 58.750 39.130 0.00 0.00 0.00 2.41
882 2622 6.494893 TGATATGTGCTTGTTTACACCTTC 57.505 37.500 0.00 0.00 35.90 3.46
887 2627 6.031751 TGTGCTTGTTTACACCTTCTTTTT 57.968 33.333 0.00 0.00 35.90 1.94
892 2632 7.094118 TGCTTGTTTACACCTTCTTTTTACAGT 60.094 33.333 0.00 0.00 0.00 3.55
951 2691 0.784778 CGCGGACTCTCTTTTGTGAC 59.215 55.000 0.00 0.00 0.00 3.67
1113 2853 3.931578 GCTTGAGAGCTTTCCTAGTCAA 58.068 45.455 1.16 0.00 45.65 3.18
1115 2855 5.155479 GCTTGAGAGCTTTCCTAGTCAAGG 61.155 50.000 13.98 0.00 45.40 3.61
1323 3063 4.062293 TGGACCAACATGACTTCTTTACG 58.938 43.478 0.00 0.00 0.00 3.18
1432 3172 0.034896 TCCAGAAGTTTCTCGGGCAC 59.965 55.000 9.14 0.00 34.74 5.01
1790 3530 6.815142 GCAAAATCAGTGGAAATTAGCTCATT 59.185 34.615 0.00 0.00 0.00 2.57
1838 3578 1.609555 TGTGCCCGGTGAAAAATGTAC 59.390 47.619 0.00 0.00 0.00 2.90
1885 3625 2.086869 CAAATGCCGACAGTGATTCCT 58.913 47.619 0.00 0.00 0.00 3.36
1891 3631 1.734465 CCGACAGTGATTCCTTTGCTC 59.266 52.381 0.00 0.00 0.00 4.26
2329 4072 5.152623 TGAAAGTTCTCCTGGTCTGTATG 57.847 43.478 0.00 0.00 0.00 2.39
2746 4489 2.122768 AGAGATGGGGAGTTGGCTTAG 58.877 52.381 0.00 0.00 0.00 2.18
2773 4516 9.877178 CATCTAGCTAACATAGTAAATAAGGGG 57.123 37.037 0.00 0.00 0.00 4.79
2788 4531 3.385193 AAGGGGAATGTTTTGCTTTCG 57.615 42.857 0.00 0.00 33.52 3.46
2850 4593 8.637196 ACAGTATCATTCGGTATCTCAATAGA 57.363 34.615 0.00 0.00 35.80 1.98
3053 4800 9.457110 CAGTCAACACAGTCTCTAATATATGTC 57.543 37.037 0.00 0.00 0.00 3.06
3058 4805 6.089476 CACAGTCTCTAATATATGTCAGCCG 58.911 44.000 0.00 0.00 0.00 5.52
3128 4875 1.903139 CAGCGTAGTTTCTACGTGACG 59.097 52.381 23.55 2.24 42.35 4.35
3156 5062 7.390440 AGCAAATTGACAAGTGTGCTATACTTA 59.610 33.333 17.01 0.00 40.40 2.24
3158 5064 9.891828 CAAATTGACAAGTGTGCTATACTTAAA 57.108 29.630 0.00 0.00 36.29 1.52
3193 5099 7.223584 TGTAGGACTGAATTTTCACAGATTCA 58.776 34.615 0.00 0.00 39.30 2.57
3204 5110 4.115401 TCACAGATTCATCGGTTCAGAG 57.885 45.455 0.00 0.00 32.93 3.35
3213 5126 3.444034 TCATCGGTTCAGAGTTCGAGATT 59.556 43.478 0.00 0.00 35.07 2.40
3214 5127 3.936372 TCGGTTCAGAGTTCGAGATTT 57.064 42.857 0.00 0.00 0.00 2.17
3215 5128 3.575630 TCGGTTCAGAGTTCGAGATTTG 58.424 45.455 0.00 0.00 0.00 2.32
3216 5129 3.254903 TCGGTTCAGAGTTCGAGATTTGA 59.745 43.478 0.00 0.00 0.00 2.69
3217 5130 3.987868 CGGTTCAGAGTTCGAGATTTGAA 59.012 43.478 2.11 2.11 0.00 2.69
3218 5131 4.447724 CGGTTCAGAGTTCGAGATTTGAAA 59.552 41.667 6.52 0.00 0.00 2.69
3219 5132 5.612709 CGGTTCAGAGTTCGAGATTTGAAAC 60.613 44.000 9.09 9.09 0.00 2.78
3418 5335 6.012745 AGGAACTTCAAAGAACAATAGGCAT 58.987 36.000 0.00 0.00 27.25 4.40
3420 5337 6.071952 GGAACTTCAAAGAACAATAGGCATGA 60.072 38.462 0.00 0.00 0.00 3.07
3466 5383 8.152023 ACCAAAACCTCTTCTAGTGATAGAAT 57.848 34.615 0.00 0.00 35.73 2.40
3477 5394 6.239396 TCTAGTGATAGAATAGGAACCGAGG 58.761 44.000 0.00 0.00 0.00 4.63
3518 5435 0.103208 CCCGTGCCTACTGCTCTTAG 59.897 60.000 0.00 0.00 42.00 2.18
3537 5454 1.703411 GAGCATCTCTAGCAGACCCT 58.297 55.000 0.00 0.00 32.26 4.34
3545 5462 6.816140 GCATCTCTAGCAGACCCTTTATATTC 59.184 42.308 0.00 0.00 32.26 1.75
3546 5463 6.576662 TCTCTAGCAGACCCTTTATATTCG 57.423 41.667 0.00 0.00 0.00 3.34
3547 5464 5.477291 TCTCTAGCAGACCCTTTATATTCGG 59.523 44.000 0.00 0.00 0.00 4.30
3548 5465 3.771577 AGCAGACCCTTTATATTCGGG 57.228 47.619 0.00 0.00 43.79 5.14
3549 5466 2.152016 GCAGACCCTTTATATTCGGGC 58.848 52.381 0.00 0.00 41.86 6.13
3550 5467 2.413837 CAGACCCTTTATATTCGGGCG 58.586 52.381 0.00 0.00 41.86 6.13
3551 5468 2.036733 CAGACCCTTTATATTCGGGCGA 59.963 50.000 0.00 0.00 41.86 5.54
3552 5469 2.701951 AGACCCTTTATATTCGGGCGAA 59.298 45.455 0.00 0.00 41.86 4.70
3553 5470 2.804527 GACCCTTTATATTCGGGCGAAC 59.195 50.000 0.00 0.00 41.86 3.95
3554 5471 1.796459 CCCTTTATATTCGGGCGAACG 59.204 52.381 0.00 0.00 36.91 3.95
3555 5472 1.796459 CCTTTATATTCGGGCGAACGG 59.204 52.381 0.00 0.00 36.91 4.44
3556 5473 2.476821 CTTTATATTCGGGCGAACGGT 58.523 47.619 0.00 0.00 36.91 4.83
3557 5474 3.552684 CCTTTATATTCGGGCGAACGGTA 60.553 47.826 0.00 0.00 36.91 4.02
3558 5475 3.724508 TTATATTCGGGCGAACGGTAA 57.275 42.857 0.00 0.00 36.91 2.85
3559 5476 2.600470 ATATTCGGGCGAACGGTAAA 57.400 45.000 0.00 0.00 36.91 2.01
3560 5477 2.376808 TATTCGGGCGAACGGTAAAA 57.623 45.000 0.00 0.00 36.91 1.52
3561 5478 1.521580 ATTCGGGCGAACGGTAAAAA 58.478 45.000 0.00 0.00 36.91 1.94
3562 5479 0.585838 TTCGGGCGAACGGTAAAAAC 59.414 50.000 0.00 0.00 0.00 2.43
3563 5480 1.207339 CGGGCGAACGGTAAAAACC 59.793 57.895 0.00 0.00 0.00 3.27
3564 5481 1.580942 GGGCGAACGGTAAAAACCC 59.419 57.895 0.00 0.00 0.00 4.11
3572 5489 0.298411 CGGTAAAAACCCGCGATACG 59.702 55.000 8.23 0.00 38.85 3.06
3581 5498 3.391355 CGCGATACGGGTTTGTCC 58.609 61.111 0.00 0.00 38.44 4.02
3603 5520 3.437642 TTTTTGGGCCAGACCAGAG 57.562 52.632 6.23 0.00 42.47 3.35
3604 5521 0.827507 TTTTTGGGCCAGACCAGAGC 60.828 55.000 6.23 0.00 42.47 4.09
3605 5522 2.713531 TTTTGGGCCAGACCAGAGCC 62.714 60.000 6.23 0.00 46.37 4.70
3609 5526 3.075005 GCCAGACCAGAGCCCGTA 61.075 66.667 0.00 0.00 0.00 4.02
3610 5527 2.435693 GCCAGACCAGAGCCCGTAT 61.436 63.158 0.00 0.00 0.00 3.06
3611 5528 1.113517 GCCAGACCAGAGCCCGTATA 61.114 60.000 0.00 0.00 0.00 1.47
3612 5529 1.633774 CCAGACCAGAGCCCGTATAT 58.366 55.000 0.00 0.00 0.00 0.86
3613 5530 1.971357 CCAGACCAGAGCCCGTATATT 59.029 52.381 0.00 0.00 0.00 1.28
3614 5531 2.028930 CCAGACCAGAGCCCGTATATTC 60.029 54.545 0.00 0.00 0.00 1.75
3615 5532 1.887198 AGACCAGAGCCCGTATATTCG 59.113 52.381 0.00 0.00 0.00 3.34
3616 5533 0.317479 ACCAGAGCCCGTATATTCGC 59.683 55.000 0.00 0.00 0.00 4.70
3617 5534 0.603569 CCAGAGCCCGTATATTCGCT 59.396 55.000 0.00 0.00 0.00 4.93
3618 5535 1.402984 CCAGAGCCCGTATATTCGCTC 60.403 57.143 8.92 8.92 46.49 5.03
3620 5537 1.983972 GAGCCCGTATATTCGCTCAG 58.016 55.000 11.09 0.00 45.64 3.35
3621 5538 0.038159 AGCCCGTATATTCGCTCAGC 60.038 55.000 0.00 0.00 0.00 4.26
3622 5539 1.014564 GCCCGTATATTCGCTCAGCC 61.015 60.000 0.00 0.00 0.00 4.85
3623 5540 0.389948 CCCGTATATTCGCTCAGCCC 60.390 60.000 0.00 0.00 0.00 5.19
3624 5541 0.732880 CCGTATATTCGCTCAGCCCG 60.733 60.000 0.00 0.00 0.00 6.13
3625 5542 0.039437 CGTATATTCGCTCAGCCCGT 60.039 55.000 0.00 0.00 0.00 5.28
3626 5543 1.699343 GTATATTCGCTCAGCCCGTC 58.301 55.000 0.00 0.00 0.00 4.79
3627 5544 1.000607 GTATATTCGCTCAGCCCGTCA 60.001 52.381 0.00 0.00 0.00 4.35
3628 5545 0.464036 ATATTCGCTCAGCCCGTCAA 59.536 50.000 0.00 0.00 0.00 3.18
3629 5546 0.248012 TATTCGCTCAGCCCGTCAAA 59.752 50.000 0.00 0.00 0.00 2.69
3630 5547 1.021390 ATTCGCTCAGCCCGTCAAAG 61.021 55.000 0.00 0.00 0.00 2.77
3631 5548 2.048222 CGCTCAGCCCGTCAAAGA 60.048 61.111 0.00 0.00 0.00 2.52
3632 5549 1.448540 CGCTCAGCCCGTCAAAGAT 60.449 57.895 0.00 0.00 0.00 2.40
3633 5550 1.021390 CGCTCAGCCCGTCAAAGATT 61.021 55.000 0.00 0.00 0.00 2.40
3634 5551 1.168714 GCTCAGCCCGTCAAAGATTT 58.831 50.000 0.00 0.00 0.00 2.17
3635 5552 1.541588 GCTCAGCCCGTCAAAGATTTT 59.458 47.619 0.00 0.00 0.00 1.82
3636 5553 2.747446 GCTCAGCCCGTCAAAGATTTTA 59.253 45.455 0.00 0.00 0.00 1.52
3637 5554 3.426292 GCTCAGCCCGTCAAAGATTTTAC 60.426 47.826 0.00 0.00 0.00 2.01
3638 5555 3.745799 TCAGCCCGTCAAAGATTTTACA 58.254 40.909 0.00 0.00 0.00 2.41
3639 5556 3.751175 TCAGCCCGTCAAAGATTTTACAG 59.249 43.478 0.00 0.00 0.00 2.74
3640 5557 3.502211 CAGCCCGTCAAAGATTTTACAGT 59.498 43.478 0.00 0.00 0.00 3.55
3641 5558 3.502211 AGCCCGTCAAAGATTTTACAGTG 59.498 43.478 0.00 0.00 0.00 3.66
3642 5559 3.365969 GCCCGTCAAAGATTTTACAGTGG 60.366 47.826 0.00 0.00 0.00 4.00
3643 5560 3.365969 CCCGTCAAAGATTTTACAGTGGC 60.366 47.826 0.00 0.00 0.00 5.01
3644 5561 3.365969 CCGTCAAAGATTTTACAGTGGCC 60.366 47.826 0.00 0.00 0.00 5.36
3645 5562 3.365969 CGTCAAAGATTTTACAGTGGCCC 60.366 47.826 0.00 0.00 0.00 5.80
3646 5563 2.817258 TCAAAGATTTTACAGTGGCCCG 59.183 45.455 0.00 0.00 0.00 6.13
3647 5564 1.173913 AAGATTTTACAGTGGCCCGC 58.826 50.000 0.00 0.00 0.00 6.13
3648 5565 0.037590 AGATTTTACAGTGGCCCGCA 59.962 50.000 0.00 0.00 0.00 5.69
3649 5566 0.885196 GATTTTACAGTGGCCCGCAA 59.115 50.000 0.00 0.00 0.00 4.85
3650 5567 1.271102 GATTTTACAGTGGCCCGCAAA 59.729 47.619 0.00 0.00 0.00 3.68
3651 5568 0.386113 TTTTACAGTGGCCCGCAAAC 59.614 50.000 0.00 0.00 0.00 2.93
3652 5569 1.457009 TTTACAGTGGCCCGCAAACC 61.457 55.000 0.00 0.00 0.00 3.27
3677 5594 3.413522 GCCCACGCGGTATATCTAC 57.586 57.895 12.47 0.00 0.00 2.59
3678 5595 0.455633 GCCCACGCGGTATATCTACG 60.456 60.000 12.47 0.00 0.00 3.51
3679 5596 0.169672 CCCACGCGGTATATCTACGG 59.830 60.000 12.47 0.00 0.00 4.02
3680 5597 0.169672 CCACGCGGTATATCTACGGG 59.830 60.000 12.47 0.00 44.60 5.28
3681 5598 3.329300 ACGCGGTATATCTACGGGT 57.671 52.632 12.47 9.46 46.55 5.28
3683 5600 2.712057 CGCGGTATATCTACGGGTTT 57.288 50.000 0.00 0.00 36.08 3.27
3684 5601 2.322161 CGCGGTATATCTACGGGTTTG 58.678 52.381 0.00 0.00 36.08 2.93
3685 5602 2.064014 GCGGTATATCTACGGGTTTGC 58.936 52.381 0.00 0.00 0.00 3.68
3686 5603 2.680577 CGGTATATCTACGGGTTTGCC 58.319 52.381 0.00 0.00 0.00 4.52
3687 5604 2.680577 GGTATATCTACGGGTTTGCCG 58.319 52.381 0.00 0.00 34.97 5.69
3688 5605 2.064014 GTATATCTACGGGTTTGCCGC 58.936 52.381 0.00 0.00 34.97 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.540267 CTTTGCCCCCATTTCGTGTA 58.460 50.000 0.00 0.00 0.00 2.90
1 2 1.815817 GCTTTGCCCCCATTTCGTGT 61.816 55.000 0.00 0.00 0.00 4.49
307 313 3.070576 GCCACCAACCTGCCCATC 61.071 66.667 0.00 0.00 0.00 3.51
351 360 1.671850 CGGCTACCACGAAATCACACT 60.672 52.381 0.00 0.00 0.00 3.55
423 432 0.538287 GGGAGCACAAACTGAAGCCT 60.538 55.000 0.00 0.00 0.00 4.58
442 451 0.025001 GATCGCACATTCCACGAACG 59.975 55.000 0.00 0.00 39.56 3.95
502 512 1.074889 ACTAACCCCACCAGCGAAAAT 59.925 47.619 0.00 0.00 0.00 1.82
524 534 7.705752 TGTACGATCAACTAGACAGTAGACTAG 59.294 40.741 0.00 0.00 43.04 2.57
608 621 7.211573 TCTCTTCCAAACAGTAAACGTATCAA 58.788 34.615 0.00 0.00 0.00 2.57
687 701 2.738964 GCCTCCAGTGATCGAACTAACC 60.739 54.545 0.00 0.00 0.00 2.85
842 2582 5.247110 ACATATCAGCGAGATAGAACCCAAT 59.753 40.000 7.74 0.00 42.26 3.16
849 2589 4.279420 ACAAGCACATATCAGCGAGATAGA 59.721 41.667 7.74 0.00 42.26 1.98
877 2617 8.652290 AGTAGAAGATCACTGTAAAAAGAAGGT 58.348 33.333 0.00 0.00 0.00 3.50
887 2627 7.283354 CACACTATCCAGTAGAAGATCACTGTA 59.717 40.741 9.37 0.00 40.47 2.74
892 2632 5.519808 ACCACACTATCCAGTAGAAGATCA 58.480 41.667 0.00 0.00 34.38 2.92
951 2691 5.336150 ACACCAATCAGTATCAGAGACAG 57.664 43.478 0.00 0.00 0.00 3.51
1113 2853 1.078848 GCAGTCATCGGCAGAACCT 60.079 57.895 0.00 0.00 35.61 3.50
1115 2855 1.014044 TTCGCAGTCATCGGCAGAAC 61.014 55.000 0.00 0.00 34.60 3.01
1317 3057 2.599082 GAGCTCCGTCATTGTCGTAAAG 59.401 50.000 0.87 0.00 0.00 1.85
1323 3063 2.266554 CTCAAGAGCTCCGTCATTGTC 58.733 52.381 10.93 0.00 0.00 3.18
1398 3138 5.186198 ACTTCTGGAGAATAAAATCCACCG 58.814 41.667 0.00 0.00 40.70 4.94
1432 3172 7.757173 TCTCTGAAAGTTCATCAGTAATTCTCG 59.243 37.037 4.82 0.00 43.77 4.04
1790 3530 6.708502 TCGAAGGTGAAAAATGTGACTATTCA 59.291 34.615 0.00 0.00 0.00 2.57
1838 3578 1.801025 GCACGACTTTTGGTGGTTTGG 60.801 52.381 0.00 0.00 34.69 3.28
1891 3631 3.319689 TGATGTATTCCTGCATTGCCATG 59.680 43.478 6.12 0.00 0.00 3.66
2329 4072 2.877691 GCCAATGGCGGTTCTCAC 59.122 61.111 9.14 0.00 39.62 3.51
2746 4489 9.372369 CCCTTATTTACTATGTTAGCTAGATGC 57.628 37.037 0.00 0.00 43.29 3.91
2773 4516 2.097444 CGCAACCGAAAGCAAAACATTC 60.097 45.455 0.00 0.00 36.29 2.67
2788 4531 0.454452 GCCAATTCGACTTCGCAACC 60.454 55.000 0.35 0.00 39.60 3.77
2955 4698 2.005451 CACAGAGAAATCTGAAGCCCG 58.995 52.381 12.00 0.00 39.99 6.13
3053 4800 6.806249 ACAATTACATTTCACATAAACGGCTG 59.194 34.615 0.00 0.00 0.00 4.85
3128 4875 3.709987 AGCACACTTGTCAATTTGCTTC 58.290 40.909 9.00 0.00 36.97 3.86
3172 5078 6.253746 CGATGAATCTGTGAAAATTCAGTCC 58.746 40.000 0.00 0.00 43.15 3.85
3193 5099 4.082190 TCAAATCTCGAACTCTGAACCGAT 60.082 41.667 0.00 0.00 0.00 4.18
3204 5110 7.376072 ACGAATTTCAAGTTTCAAATCTCGAAC 59.624 33.333 17.33 0.00 32.70 3.95
3213 5126 8.836413 AGAGATAACACGAATTTCAAGTTTCAA 58.164 29.630 8.26 0.00 0.00 2.69
3214 5127 8.378172 AGAGATAACACGAATTTCAAGTTTCA 57.622 30.769 8.26 0.00 0.00 2.69
3215 5128 9.959775 CTAGAGATAACACGAATTTCAAGTTTC 57.040 33.333 8.26 6.79 0.00 2.78
3216 5129 8.443937 GCTAGAGATAACACGAATTTCAAGTTT 58.556 33.333 8.26 0.00 0.00 2.66
3217 5130 7.602644 TGCTAGAGATAACACGAATTTCAAGTT 59.397 33.333 0.00 8.09 0.00 2.66
3218 5131 7.097192 TGCTAGAGATAACACGAATTTCAAGT 58.903 34.615 0.00 0.00 0.00 3.16
3219 5132 7.525688 TGCTAGAGATAACACGAATTTCAAG 57.474 36.000 0.00 0.00 0.00 3.02
3400 5317 5.649395 CCTCTCATGCCTATTGTTCTTTGAA 59.351 40.000 0.00 0.00 0.00 2.69
3401 5318 5.188434 CCTCTCATGCCTATTGTTCTTTGA 58.812 41.667 0.00 0.00 0.00 2.69
3418 5335 1.221840 GCTTTCCGGATGCCTCTCA 59.778 57.895 4.15 0.00 0.00 3.27
3420 5337 1.267574 TGAGCTTTCCGGATGCCTCT 61.268 55.000 21.53 8.67 0.00 3.69
3466 5383 2.105766 GCCTAAAGACCTCGGTTCCTA 58.894 52.381 0.00 0.00 0.00 2.94
3477 5394 5.163509 GGGAAAATGATGGAAGCCTAAAGAC 60.164 44.000 0.00 0.00 0.00 3.01
3518 5435 1.703411 AGGGTCTGCTAGAGATGCTC 58.297 55.000 0.00 0.00 31.63 4.26
3530 5447 2.036733 TCGCCCGAATATAAAGGGTCTG 59.963 50.000 10.60 3.64 46.69 3.51
3537 5454 2.600470 ACCGTTCGCCCGAATATAAA 57.400 45.000 6.38 0.00 36.45 1.40
3545 5462 1.207339 GGTTTTTACCGTTCGCCCG 59.793 57.895 0.00 0.00 0.00 6.13
3546 5463 1.580942 GGGTTTTTACCGTTCGCCC 59.419 57.895 0.00 0.00 0.00 6.13
3547 5464 1.207339 CGGGTTTTTACCGTTCGCC 59.793 57.895 0.00 0.00 46.03 5.54
3548 5465 4.824550 CGGGTTTTTACCGTTCGC 57.175 55.556 0.00 0.00 46.03 4.70
3564 5481 3.391355 GGACAAACCCGTATCGCG 58.609 61.111 0.00 0.00 40.95 5.87
3585 5502 0.827507 GCTCTGGTCTGGCCCAAAAA 60.828 55.000 0.00 0.00 33.07 1.94
3586 5503 1.228552 GCTCTGGTCTGGCCCAAAA 60.229 57.895 0.00 0.00 33.07 2.44
3587 5504 2.436109 GCTCTGGTCTGGCCCAAA 59.564 61.111 0.00 0.00 33.07 3.28
3588 5505 3.650950 GGCTCTGGTCTGGCCCAA 61.651 66.667 0.00 0.00 39.96 4.12
3592 5509 1.113517 TATACGGGCTCTGGTCTGGC 61.114 60.000 0.00 0.00 0.00 4.85
3593 5510 1.633774 ATATACGGGCTCTGGTCTGG 58.366 55.000 0.00 0.00 0.00 3.86
3594 5511 2.351835 CGAATATACGGGCTCTGGTCTG 60.352 54.545 0.00 0.00 0.00 3.51
3595 5512 1.887198 CGAATATACGGGCTCTGGTCT 59.113 52.381 0.00 0.00 0.00 3.85
3596 5513 1.669211 GCGAATATACGGGCTCTGGTC 60.669 57.143 0.00 0.00 0.00 4.02
3597 5514 0.317479 GCGAATATACGGGCTCTGGT 59.683 55.000 0.00 0.00 0.00 4.00
3598 5515 0.603569 AGCGAATATACGGGCTCTGG 59.396 55.000 0.00 0.00 0.00 3.86
3599 5516 1.983972 GAGCGAATATACGGGCTCTG 58.016 55.000 11.49 0.00 46.33 3.35
3602 5519 0.038159 GCTGAGCGAATATACGGGCT 60.038 55.000 0.00 0.00 38.70 5.19
3603 5520 1.014564 GGCTGAGCGAATATACGGGC 61.015 60.000 0.00 0.00 0.00 6.13
3604 5521 0.389948 GGGCTGAGCGAATATACGGG 60.390 60.000 0.00 0.00 0.00 5.28
3605 5522 0.732880 CGGGCTGAGCGAATATACGG 60.733 60.000 0.00 0.00 0.00 4.02
3606 5523 0.039437 ACGGGCTGAGCGAATATACG 60.039 55.000 0.00 0.00 0.00 3.06
3607 5524 1.000607 TGACGGGCTGAGCGAATATAC 60.001 52.381 0.00 0.00 0.00 1.47
3608 5525 1.324383 TGACGGGCTGAGCGAATATA 58.676 50.000 0.00 0.00 0.00 0.86
3609 5526 0.464036 TTGACGGGCTGAGCGAATAT 59.536 50.000 0.00 0.00 0.00 1.28
3610 5527 0.248012 TTTGACGGGCTGAGCGAATA 59.752 50.000 0.00 0.00 0.00 1.75
3611 5528 1.003839 TTTGACGGGCTGAGCGAAT 60.004 52.632 0.00 0.00 0.00 3.34
3612 5529 1.667830 CTTTGACGGGCTGAGCGAA 60.668 57.895 0.00 0.00 0.00 4.70
3613 5530 1.888436 ATCTTTGACGGGCTGAGCGA 61.888 55.000 0.00 0.00 0.00 4.93
3614 5531 1.021390 AATCTTTGACGGGCTGAGCG 61.021 55.000 0.00 0.00 0.00 5.03
3615 5532 1.168714 AAATCTTTGACGGGCTGAGC 58.831 50.000 0.00 0.00 0.00 4.26
3616 5533 3.751175 TGTAAAATCTTTGACGGGCTGAG 59.249 43.478 0.00 0.00 0.00 3.35
3617 5534 3.745799 TGTAAAATCTTTGACGGGCTGA 58.254 40.909 0.00 0.00 0.00 4.26
3618 5535 3.502211 ACTGTAAAATCTTTGACGGGCTG 59.498 43.478 4.41 0.00 33.03 4.85
3619 5536 3.502211 CACTGTAAAATCTTTGACGGGCT 59.498 43.478 4.41 0.00 33.03 5.19
3620 5537 3.365969 CCACTGTAAAATCTTTGACGGGC 60.366 47.826 4.41 0.00 33.03 6.13
3621 5538 3.365969 GCCACTGTAAAATCTTTGACGGG 60.366 47.826 4.41 0.00 33.03 5.28
3622 5539 3.365969 GGCCACTGTAAAATCTTTGACGG 60.366 47.826 0.00 0.00 34.61 4.79
3623 5540 3.365969 GGGCCACTGTAAAATCTTTGACG 60.366 47.826 4.39 0.00 0.00 4.35
3624 5541 3.365969 CGGGCCACTGTAAAATCTTTGAC 60.366 47.826 4.39 0.00 0.00 3.18
3625 5542 2.817258 CGGGCCACTGTAAAATCTTTGA 59.183 45.455 4.39 0.00 0.00 2.69
3626 5543 2.671070 GCGGGCCACTGTAAAATCTTTG 60.671 50.000 4.39 0.00 0.00 2.77
3627 5544 1.544246 GCGGGCCACTGTAAAATCTTT 59.456 47.619 4.39 0.00 0.00 2.52
3628 5545 1.173913 GCGGGCCACTGTAAAATCTT 58.826 50.000 4.39 0.00 0.00 2.40
3629 5546 0.037590 TGCGGGCCACTGTAAAATCT 59.962 50.000 4.39 0.00 0.00 2.40
3630 5547 0.885196 TTGCGGGCCACTGTAAAATC 59.115 50.000 4.39 0.00 0.00 2.17
3631 5548 1.000394 GTTTGCGGGCCACTGTAAAAT 60.000 47.619 4.39 0.00 38.91 1.82
3632 5549 0.386113 GTTTGCGGGCCACTGTAAAA 59.614 50.000 4.39 0.00 38.91 1.52
3633 5550 1.457009 GGTTTGCGGGCCACTGTAAA 61.457 55.000 4.39 2.83 35.58 2.01
3634 5551 1.899534 GGTTTGCGGGCCACTGTAA 60.900 57.895 4.39 0.00 0.00 2.41
3635 5552 2.281900 GGTTTGCGGGCCACTGTA 60.282 61.111 4.39 0.00 0.00 2.74
3659 5576 0.455633 CGTAGATATACCGCGTGGGC 60.456 60.000 21.14 3.02 40.62 5.36
3660 5577 0.169672 CCGTAGATATACCGCGTGGG 59.830 60.000 21.14 6.53 40.75 4.61
3661 5578 0.169672 CCCGTAGATATACCGCGTGG 59.830 60.000 14.93 14.93 42.84 4.94
3662 5579 0.877071 ACCCGTAGATATACCGCGTG 59.123 55.000 4.92 0.00 0.00 5.34
3663 5580 1.609208 AACCCGTAGATATACCGCGT 58.391 50.000 4.92 0.00 0.00 6.01
3664 5581 2.322161 CAAACCCGTAGATATACCGCG 58.678 52.381 0.00 0.00 0.00 6.46
3665 5582 2.064014 GCAAACCCGTAGATATACCGC 58.936 52.381 0.00 0.00 0.00 5.68
3666 5583 2.680577 GGCAAACCCGTAGATATACCG 58.319 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.