Multiple sequence alignment - TraesCS3D01G360700

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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 TraesCS3D01G360700 chr3D 100.000 4477 0 0 1 4477 474426796 474431272 0.000000e+00 8268.0
1 TraesCS3D01G360700 chr3B 95.571 3545 112 21 969 4477 630586854 630590389 0.000000e+00 5635.0
2 TraesCS3D01G360700 chr3B 96.055 2180 54 6 891 3043 630586751 630588925 0.000000e+00 3520.0
3 TraesCS3D01G360700 chr3B 82.048 908 129 24 2 891 630536565 630537456 0.000000e+00 743.0
4 TraesCS3D01G360700 chr3A 96.295 3428 106 10 774 4196 616704308 616707719 0.000000e+00 5607.0
5 TraesCS3D01G360700 chr3A 89.826 403 35 5 377 777 616666770 616667168 3.090000e-141 512.0
6 TraesCS3D01G360700 chr3A 89.211 380 27 6 3 380 616665631 616665998 3.150000e-126 462.0
7 TraesCS3D01G360700 chr3A 92.278 259 11 3 4185 4435 616708927 616709184 4.260000e-95 359.0
8 TraesCS3D01G360700 chr2D 84.211 76 11 1 4174 4249 305938906 305938832 6.210000e-09 73.1
9 TraesCS3D01G360700 chr2A 85.075 67 8 1 4176 4240 384969602 384969536 2.890000e-07 67.6


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 TraesCS3D01G360700 chr3D 474426796 474431272 4476 False 8268.0 8268 100.0000 1 4477 1 chr3D.!!$F1 4476
1 TraesCS3D01G360700 chr3B 630586751 630590389 3638 False 4577.5 5635 95.8130 891 4477 2 chr3B.!!$F2 3586
2 TraesCS3D01G360700 chr3B 630536565 630537456 891 False 743.0 743 82.0480 2 891 1 chr3B.!!$F1 889
3 TraesCS3D01G360700 chr3A 616704308 616709184 4876 False 2983.0 5607 94.2865 774 4435 2 chr3A.!!$F2 3661
4 TraesCS3D01G360700 chr3A 616665631 616667168 1537 False 487.0 512 89.5185 3 777 2 chr3A.!!$F1 774

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
440 461 0.108804 TGCCTTCGATGACGGAAGAC 60.109 55.000 0.00 0.00 40.21 3.01 F
447 468 0.179000 GATGACGGAAGACCAGCCAT 59.821 55.000 0.00 0.00 35.59 4.40 F
455 476 0.251787 AAGACCAGCCATTTGGGACC 60.252 55.000 0.00 0.00 42.76 4.46 F
1827 1912 0.179045 GTGTTGGGATAGCGGCTGAT 60.179 55.000 13.86 2.17 0.00 2.90 F
1899 1984 1.268743 GCACAAGGTCAGCAAGTTCAC 60.269 52.381 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1895 0.179045 ACATCAGCCGCTATCCCAAC 60.179 55.000 0.0 0.0 0.00 3.77 R
1816 1901 0.179073 GTGACCACATCAGCCGCTAT 60.179 55.000 0.0 0.0 38.28 2.97 R
1899 1984 0.729116 CAGCCTTGATAACCTGTGCG 59.271 55.000 0.0 0.0 0.00 5.34 R
3445 4197 0.842467 AAGGACCAGAACCTCCAGGG 60.842 60.000 0.0 0.0 40.27 4.45 R
3504 4256 1.747355 GCTGCACTATTGTTGCTCCAT 59.253 47.619 0.0 0.0 0.00 3.41 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
62 63 0.250166 GAAACCTAGCCACCACACGT 60.250 55.000 0.00 0.00 0.00 4.49
111 113 3.644953 AGGGATTCCTCTCCTCCAC 57.355 57.895 2.01 0.00 39.80 4.02
194 196 8.809066 TGTTCAATAGTCTAGTGGCTTAGTTAA 58.191 33.333 7.44 0.00 0.00 2.01
205 207 4.507021 GTGGCTTAGTTAACTATTCGCCTC 59.493 45.833 30.54 26.75 37.45 4.70
206 208 3.734735 GGCTTAGTTAACTATTCGCCTCG 59.265 47.826 27.21 10.24 35.55 4.63
281 290 4.569943 TCTCTCAGCTATTGGTGTTGAAC 58.430 43.478 6.25 0.00 41.91 3.18
292 302 1.470051 GTGTTGAACCTGGTTGTGGT 58.530 50.000 18.42 0.00 39.91 4.16
309 319 1.003839 GTGTCTGCAATGTCCCGGA 60.004 57.895 0.73 0.00 0.00 5.14
401 422 0.462937 TCTTTGTGGTGGTGGTGACG 60.463 55.000 0.00 0.00 0.00 4.35
409 430 1.450491 TGGTGGTGACGTGGTGTTG 60.450 57.895 0.00 0.00 0.00 3.33
421 442 2.807676 GTGGTGTTGAGGGAATCCAAT 58.192 47.619 0.09 0.00 34.83 3.16
432 453 2.575532 GGAATCCAATGCCTTCGATGA 58.424 47.619 0.00 0.00 0.00 2.92
433 454 2.291741 GGAATCCAATGCCTTCGATGAC 59.708 50.000 0.00 0.00 0.00 3.06
434 455 1.586422 ATCCAATGCCTTCGATGACG 58.414 50.000 0.00 0.00 41.26 4.35
439 460 0.824109 ATGCCTTCGATGACGGAAGA 59.176 50.000 0.00 0.00 40.21 2.87
440 461 0.108804 TGCCTTCGATGACGGAAGAC 60.109 55.000 0.00 0.00 40.21 3.01
446 467 1.596934 GATGACGGAAGACCAGCCA 59.403 57.895 0.00 0.00 35.59 4.75
447 468 0.179000 GATGACGGAAGACCAGCCAT 59.821 55.000 0.00 0.00 35.59 4.40
455 476 0.251787 AAGACCAGCCATTTGGGACC 60.252 55.000 0.00 0.00 42.76 4.46
459 480 1.606313 CAGCCATTTGGGACCGGTT 60.606 57.895 9.42 0.00 40.01 4.44
460 481 1.155155 AGCCATTTGGGACCGGTTT 59.845 52.632 9.42 0.00 40.01 3.27
468 489 1.611519 TGGGACCGGTTTGATGTTTC 58.388 50.000 9.42 0.00 0.00 2.78
473 494 1.570347 CCGGTTTGATGTTTCCGCGA 61.570 55.000 8.23 0.00 41.38 5.87
474 495 0.452122 CGGTTTGATGTTTCCGCGAC 60.452 55.000 8.23 0.00 36.68 5.19
481 502 0.664224 ATGTTTCCGCGACCGTTTTT 59.336 45.000 8.23 0.00 0.00 1.94
515 536 3.933332 CGAGGTTGTGGTCTCCTTTTATC 59.067 47.826 0.00 0.00 0.00 1.75
522 543 5.560724 TGTGGTCTCCTTTTATCTCTTTGG 58.439 41.667 0.00 0.00 0.00 3.28
525 546 4.944317 GGTCTCCTTTTATCTCTTTGGGTG 59.056 45.833 0.00 0.00 0.00 4.61
529 550 7.014326 GTCTCCTTTTATCTCTTTGGGTGTTTT 59.986 37.037 0.00 0.00 0.00 2.43
537 558 4.037923 TCTCTTTGGGTGTTTTCTTGATGC 59.962 41.667 0.00 0.00 0.00 3.91
542 563 2.228822 GGGTGTTTTCTTGATGCGACAT 59.771 45.455 0.00 0.00 0.00 3.06
545 566 5.393027 GGGTGTTTTCTTGATGCGACATAAT 60.393 40.000 0.00 0.00 0.00 1.28
554 575 3.688673 TGATGCGACATAATGCTTTGTGA 59.311 39.130 14.67 0.00 0.00 3.58
569 590 4.315803 CTTTGTGACGGTTCATACTTCCT 58.684 43.478 0.00 0.00 33.11 3.36
572 593 3.576982 TGTGACGGTTCATACTTCCTCTT 59.423 43.478 0.00 0.00 33.11 2.85
573 594 4.039973 TGTGACGGTTCATACTTCCTCTTT 59.960 41.667 0.00 0.00 33.11 2.52
574 595 4.389077 GTGACGGTTCATACTTCCTCTTTG 59.611 45.833 0.00 0.00 33.11 2.77
578 599 5.930569 ACGGTTCATACTTCCTCTTTGTTAC 59.069 40.000 0.00 0.00 0.00 2.50
584 605 3.477530 ACTTCCTCTTTGTTACAGTGGC 58.522 45.455 0.00 0.00 0.00 5.01
588 609 1.461127 CTCTTTGTTACAGTGGCGCTC 59.539 52.381 7.64 0.45 0.00 5.03
590 611 1.873591 CTTTGTTACAGTGGCGCTCTT 59.126 47.619 7.64 0.00 0.00 2.85
591 612 1.508632 TTGTTACAGTGGCGCTCTTC 58.491 50.000 7.64 0.00 0.00 2.87
592 613 0.679505 TGTTACAGTGGCGCTCTTCT 59.320 50.000 7.64 0.00 0.00 2.85
593 614 1.890489 TGTTACAGTGGCGCTCTTCTA 59.110 47.619 7.64 0.00 0.00 2.10
594 615 2.260481 GTTACAGTGGCGCTCTTCTAC 58.740 52.381 7.64 0.00 0.00 2.59
595 616 1.835494 TACAGTGGCGCTCTTCTACT 58.165 50.000 7.64 0.00 0.00 2.57
596 617 1.835494 ACAGTGGCGCTCTTCTACTA 58.165 50.000 7.64 0.00 0.00 1.82
597 618 1.473278 ACAGTGGCGCTCTTCTACTAC 59.527 52.381 7.64 0.00 0.00 2.73
599 620 1.746220 AGTGGCGCTCTTCTACTACTG 59.254 52.381 7.64 0.00 0.00 2.74
600 621 1.473278 GTGGCGCTCTTCTACTACTGT 59.527 52.381 7.64 0.00 0.00 3.55
602 623 2.094700 TGGCGCTCTTCTACTACTGTTG 60.095 50.000 7.64 0.00 0.00 3.33
604 625 2.671351 GCGCTCTTCTACTACTGTTGCA 60.671 50.000 0.00 0.00 0.00 4.08
611 633 6.578944 TCTTCTACTACTGTTGCAAAGTTGA 58.421 36.000 20.60 15.28 0.00 3.18
638 660 2.456577 TCATGAGATGGTTCAGGTCGA 58.543 47.619 0.00 0.00 31.24 4.20
643 665 4.474394 TGAGATGGTTCAGGTCGATCTAT 58.526 43.478 0.00 0.00 32.24 1.98
657 709 7.433719 CAGGTCGATCTATACAAAAGACTTCTG 59.566 40.741 0.00 0.00 0.00 3.02
662 714 8.607459 CGATCTATACAAAAGACTTCTGCATTT 58.393 33.333 0.00 0.00 0.00 2.32
675 727 3.674997 TCTGCATTTACGGCTTCTTCTT 58.325 40.909 0.00 0.00 0.00 2.52
677 729 3.407698 TGCATTTACGGCTTCTTCTTCA 58.592 40.909 0.00 0.00 0.00 3.02
678 730 4.009675 TGCATTTACGGCTTCTTCTTCAT 58.990 39.130 0.00 0.00 0.00 2.57
679 731 5.182487 TGCATTTACGGCTTCTTCTTCATA 58.818 37.500 0.00 0.00 0.00 2.15
688 740 4.393371 GGCTTCTTCTTCATAGTGTTGGTC 59.607 45.833 0.00 0.00 0.00 4.02
703 755 0.392461 TGGTCCAGCCGAACATTAGC 60.392 55.000 0.00 0.00 41.21 3.09
706 758 0.392461 TCCAGCCGAACATTAGCACC 60.392 55.000 0.00 0.00 0.00 5.01
722 774 1.063174 GCACCATGACTTCTCAATCGC 59.937 52.381 0.00 0.00 0.00 4.58
724 776 2.941064 CACCATGACTTCTCAATCGCAT 59.059 45.455 0.00 0.00 0.00 4.73
726 778 4.753610 CACCATGACTTCTCAATCGCATAT 59.246 41.667 0.00 0.00 0.00 1.78
727 779 5.928264 CACCATGACTTCTCAATCGCATATA 59.072 40.000 0.00 0.00 0.00 0.86
729 781 7.118825 CACCATGACTTCTCAATCGCATATAAT 59.881 37.037 0.00 0.00 0.00 1.28
730 782 8.314021 ACCATGACTTCTCAATCGCATATAATA 58.686 33.333 0.00 0.00 0.00 0.98
731 783 8.598924 CCATGACTTCTCAATCGCATATAATAC 58.401 37.037 0.00 0.00 0.00 1.89
732 784 8.598924 CATGACTTCTCAATCGCATATAATACC 58.401 37.037 0.00 0.00 0.00 2.73
733 785 7.666623 TGACTTCTCAATCGCATATAATACCA 58.333 34.615 0.00 0.00 0.00 3.25
734 786 8.314021 TGACTTCTCAATCGCATATAATACCAT 58.686 33.333 0.00 0.00 0.00 3.55
744 796 9.836864 ATCGCATATAATACCATAATGTCATGT 57.163 29.630 0.00 0.00 0.00 3.21
748 800 6.985188 ATAATACCATAATGTCATGTCGGC 57.015 37.500 0.00 0.00 0.00 5.54
749 801 2.708216 ACCATAATGTCATGTCGGCA 57.292 45.000 0.00 0.00 0.00 5.69
750 802 2.288666 ACCATAATGTCATGTCGGCAC 58.711 47.619 0.00 0.00 0.00 5.01
751 803 1.603802 CCATAATGTCATGTCGGCACC 59.396 52.381 0.00 0.00 0.00 5.01
764 816 1.561717 CGGCACCGACAATGAAACGA 61.562 55.000 2.01 0.00 42.83 3.85
771 823 1.396996 CGACAATGAAACGATGGGGAC 59.603 52.381 0.00 0.00 0.00 4.46
869 927 9.736023 ATGTCTTGTATTGTTGAAAGAAAGTTC 57.264 29.630 0.00 0.00 30.85 3.01
1137 1222 1.975407 GGACGTCCTCTGGTCGGAA 60.975 63.158 27.64 0.00 38.44 4.30
1322 1407 2.295253 TTCGAGAGAATTCCGAAGCC 57.705 50.000 12.20 0.00 46.92 4.35
1353 1438 3.074390 TGTCCTGGAACATTCTGATTGGT 59.926 43.478 0.00 0.00 38.20 3.67
1412 1497 1.086696 CTGTTCGACGAAATGCCCAT 58.913 50.000 12.67 0.00 0.00 4.00
1466 1551 2.677524 GCTCACCAATGCAGGGCA 60.678 61.111 7.09 0.00 44.86 5.36
1563 1648 4.641645 TTCAGGTGCTGTGCCGGG 62.642 66.667 2.18 0.00 32.61 5.73
1606 1691 1.901591 CCAGGTCCATGCATATGTCC 58.098 55.000 0.00 1.05 32.21 4.02
1641 1726 2.884012 GGACATTGACATGTGTGTTGGA 59.116 45.455 1.15 0.00 44.22 3.53
1680 1765 4.722700 ATGCGGTGTGGGTGCCTC 62.723 66.667 0.00 0.00 0.00 4.70
1794 1879 3.545703 CGAGGGAGCATTGGAGTATTTT 58.454 45.455 0.00 0.00 0.00 1.82
1810 1895 6.261826 GGAGTATTTTTCCATGATGAGAGGTG 59.738 42.308 0.00 0.00 34.74 4.00
1816 1901 1.561076 CCATGATGAGAGGTGTTGGGA 59.439 52.381 0.00 0.00 0.00 4.37
1827 1912 0.179045 GTGTTGGGATAGCGGCTGAT 60.179 55.000 13.86 2.17 0.00 2.90
1899 1984 1.268743 GCACAAGGTCAGCAAGTTCAC 60.269 52.381 0.00 0.00 0.00 3.18
1974 2059 3.642705 TGTGCATATGTACTCTCGATGC 58.357 45.455 22.21 3.13 42.57 3.91
2503 2588 2.114616 GATGGGGAGATGTCAGTGAGT 58.885 52.381 0.00 0.00 0.00 3.41
2626 2711 4.356436 TCATCCAAGACAAGGAGAGATCA 58.644 43.478 0.00 0.00 38.83 2.92
2953 3038 5.191522 TCCTGTGGAGATTATTGGTGATGAA 59.808 40.000 0.00 0.00 0.00 2.57
2982 3067 6.772716 ACTCAACTGTGTGTATCTTTTCCATT 59.227 34.615 0.00 0.00 29.78 3.16
2988 3073 4.622740 GTGTGTATCTTTTCCATTTGCTGC 59.377 41.667 0.00 0.00 0.00 5.25
3181 3677 9.577110 TCAAAAATAAATGCATTCACTCTGATC 57.423 29.630 13.38 0.00 0.00 2.92
3188 3684 4.654915 TGCATTCACTCTGATCCTCAAAA 58.345 39.130 0.00 0.00 0.00 2.44
3189 3685 5.072055 TGCATTCACTCTGATCCTCAAAAA 58.928 37.500 0.00 0.00 0.00 1.94
3190 3686 5.713389 TGCATTCACTCTGATCCTCAAAAAT 59.287 36.000 0.00 0.00 0.00 1.82
3271 3767 7.893124 ATTCTGAAGTTCAGGATATGCATTT 57.107 32.000 28.33 0.00 40.83 2.32
3445 4197 0.737219 GGATCATGTGTTGCTGGAGC 59.263 55.000 0.00 0.00 42.50 4.70
3459 4211 2.674220 GGAGCCCTGGAGGTTCTGG 61.674 68.421 0.00 0.00 45.00 3.86
3472 4224 2.158234 AGGTTCTGGTCCTTCTGAGAGT 60.158 50.000 0.00 0.00 30.18 3.24
3481 4233 4.142271 GGTCCTTCTGAGAGTATGACAGTG 60.142 50.000 0.00 0.00 33.93 3.66
3504 4256 6.259167 GTGGAAACTATCGGTGCAATTATACA 59.741 38.462 0.00 0.00 0.00 2.29
3559 4311 5.299531 GGAAGGCAAGTGTCTCTTTTACTTT 59.700 40.000 0.00 0.00 32.69 2.66
3850 4602 3.078837 GTTTGCAGATTCCTCGGGTTTA 58.921 45.455 0.00 0.00 0.00 2.01
3927 4679 3.381272 TGCAGAAAGGTTATTATGCTGCC 59.619 43.478 0.00 0.00 45.33 4.85
3969 4723 4.107311 TGAGGGTTTCTTTACCTTGGGAAT 59.893 41.667 0.00 0.00 38.30 3.01
4154 4908 1.709578 TTTTGGCCTGGCACAATACA 58.290 45.000 22.05 4.88 38.70 2.29
4196 4950 1.001393 TGGAACAAAGCCGATCCCC 60.001 57.895 0.00 0.00 31.92 4.81
4361 6334 3.909086 GAAGCGGCTCACAAGGGCT 62.909 63.158 1.45 0.00 35.01 5.19
4367 6343 0.600057 GGCTCACAAGGGCTCAAAAG 59.400 55.000 0.00 0.00 0.00 2.27
4437 6418 2.790791 CCAAGCCGATCCTCGAGCT 61.791 63.158 6.99 0.00 43.74 4.09
4461 6442 1.300620 CTTCGGACTGGCACGACAA 60.301 57.895 0.00 0.00 39.04 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.165890 ACGTGTTACATATGTGACGTCG 58.834 45.455 28.34 28.34 37.35 5.12
34 35 1.281867 TGGCTAGGTTTCACAGGGATG 59.718 52.381 0.00 0.00 0.00 3.51
62 63 0.405198 ATGTGGTGCATGTTCCCTCA 59.595 50.000 0.00 0.00 36.26 3.86
104 106 3.319198 GGAGCAACCGGTGGAGGA 61.319 66.667 15.02 0.00 34.73 3.71
194 196 1.135083 CCACAACTCGAGGCGAATAGT 60.135 52.381 18.41 1.33 34.74 2.12
205 207 3.853330 CGCCATCGCCACAACTCG 61.853 66.667 0.00 0.00 0.00 4.18
206 208 3.499737 CCGCCATCGCCACAACTC 61.500 66.667 0.00 0.00 0.00 3.01
281 290 0.751277 TTGCAGACACCACAACCAGG 60.751 55.000 0.00 0.00 0.00 4.45
287 296 0.537143 GGGACATTGCAGACACCACA 60.537 55.000 0.00 0.00 0.00 4.17
292 302 1.003839 GTCCGGGACATTGCAGACA 60.004 57.895 22.10 0.00 32.09 3.41
309 319 1.609210 CCGCCCAAATCCAAAGGGT 60.609 57.895 0.00 0.00 44.69 4.34
335 345 3.498082 GACATTGATACCAAAACGCACC 58.502 45.455 0.00 0.00 35.67 5.01
339 349 3.682858 ACCTCGACATTGATACCAAAACG 59.317 43.478 0.00 0.00 35.67 3.60
340 350 6.730960 TTACCTCGACATTGATACCAAAAC 57.269 37.500 0.00 0.00 35.67 2.43
341 351 6.183360 GCATTACCTCGACATTGATACCAAAA 60.183 38.462 0.00 0.00 35.67 2.44
342 352 5.295787 GCATTACCTCGACATTGATACCAAA 59.704 40.000 0.00 0.00 35.67 3.28
343 353 4.814234 GCATTACCTCGACATTGATACCAA 59.186 41.667 0.00 0.00 36.61 3.67
344 354 4.100963 AGCATTACCTCGACATTGATACCA 59.899 41.667 0.00 0.00 0.00 3.25
345 355 4.632153 AGCATTACCTCGACATTGATACC 58.368 43.478 0.00 0.00 0.00 2.73
346 356 4.686554 GGAGCATTACCTCGACATTGATAC 59.313 45.833 0.00 0.00 32.57 2.24
347 357 4.588951 AGGAGCATTACCTCGACATTGATA 59.411 41.667 0.00 0.00 31.43 2.15
348 358 3.389329 AGGAGCATTACCTCGACATTGAT 59.611 43.478 0.00 0.00 31.43 2.57
349 359 2.766263 AGGAGCATTACCTCGACATTGA 59.234 45.455 0.00 0.00 31.43 2.57
401 422 2.286365 TTGGATTCCCTCAACACCAC 57.714 50.000 0.00 0.00 0.00 4.16
409 430 1.134098 TCGAAGGCATTGGATTCCCTC 60.134 52.381 0.00 0.00 0.00 4.30
421 442 0.108804 GTCTTCCGTCATCGAAGGCA 60.109 55.000 0.00 0.00 39.71 4.75
432 453 0.609131 CCAAATGGCTGGTCTTCCGT 60.609 55.000 0.00 0.00 36.30 4.69
433 454 1.315257 CCCAAATGGCTGGTCTTCCG 61.315 60.000 0.00 0.00 34.33 4.30
434 455 0.039618 TCCCAAATGGCTGGTCTTCC 59.960 55.000 0.00 0.00 34.33 3.46
439 460 2.035626 CGGTCCCAAATGGCTGGT 59.964 61.111 0.00 0.00 34.33 4.00
440 461 2.755469 CCGGTCCCAAATGGCTGG 60.755 66.667 0.00 0.00 36.10 4.85
446 467 2.302587 ACATCAAACCGGTCCCAAAT 57.697 45.000 8.04 0.00 0.00 2.32
447 468 2.074729 AACATCAAACCGGTCCCAAA 57.925 45.000 8.04 0.00 0.00 3.28
455 476 0.452122 GTCGCGGAAACATCAAACCG 60.452 55.000 6.13 0.00 46.74 4.44
459 480 0.881159 AACGGTCGCGGAAACATCAA 60.881 50.000 6.13 0.00 0.00 2.57
460 481 0.881159 AAACGGTCGCGGAAACATCA 60.881 50.000 6.13 0.00 0.00 3.07
481 502 1.225855 CAACCTCGTTGCTAGCACAA 58.774 50.000 19.17 0.00 36.73 3.33
488 509 0.249911 GAGACCACAACCTCGTTGCT 60.250 55.000 4.46 0.00 46.20 3.91
515 536 4.301628 GCATCAAGAAAACACCCAAAGAG 58.698 43.478 0.00 0.00 0.00 2.85
522 543 3.559238 ATGTCGCATCAAGAAAACACC 57.441 42.857 0.00 0.00 0.00 4.16
525 546 5.335127 AGCATTATGTCGCATCAAGAAAAC 58.665 37.500 0.00 0.00 0.00 2.43
529 550 4.395854 ACAAAGCATTATGTCGCATCAAGA 59.604 37.500 0.00 0.00 0.00 3.02
537 558 2.415168 ACCGTCACAAAGCATTATGTCG 59.585 45.455 0.00 0.00 0.00 4.35
542 563 5.242434 AGTATGAACCGTCACAAAGCATTA 58.758 37.500 0.00 0.00 36.31 1.90
545 566 3.120321 AGTATGAACCGTCACAAAGCA 57.880 42.857 0.00 0.00 36.31 3.91
554 575 4.618920 ACAAAGAGGAAGTATGAACCGT 57.381 40.909 0.00 0.00 0.00 4.83
569 590 1.070134 AGAGCGCCACTGTAACAAAGA 59.930 47.619 2.29 0.00 0.00 2.52
572 593 1.070134 AGAAGAGCGCCACTGTAACAA 59.930 47.619 2.29 0.00 0.00 2.83
573 594 0.679505 AGAAGAGCGCCACTGTAACA 59.320 50.000 2.29 0.00 0.00 2.41
574 595 2.094649 AGTAGAAGAGCGCCACTGTAAC 60.095 50.000 2.29 3.66 0.00 2.50
578 599 1.746220 AGTAGTAGAAGAGCGCCACTG 59.254 52.381 2.29 0.00 0.00 3.66
584 605 3.217599 TGCAACAGTAGTAGAAGAGCG 57.782 47.619 0.00 0.00 0.00 5.03
588 609 6.257849 TGTCAACTTTGCAACAGTAGTAGAAG 59.742 38.462 0.00 0.00 0.00 2.85
590 611 5.666462 TGTCAACTTTGCAACAGTAGTAGA 58.334 37.500 0.00 1.40 0.00 2.59
591 612 5.984233 TGTCAACTTTGCAACAGTAGTAG 57.016 39.130 0.00 0.00 0.00 2.57
592 613 6.935741 ATTGTCAACTTTGCAACAGTAGTA 57.064 33.333 0.00 0.00 30.95 1.82
593 614 5.835113 ATTGTCAACTTTGCAACAGTAGT 57.165 34.783 0.00 0.00 30.95 2.73
594 615 7.275341 TGAAAATTGTCAACTTTGCAACAGTAG 59.725 33.333 0.00 0.00 30.95 2.57
595 616 7.093354 TGAAAATTGTCAACTTTGCAACAGTA 58.907 30.769 0.00 0.00 30.95 2.74
596 617 5.931146 TGAAAATTGTCAACTTTGCAACAGT 59.069 32.000 0.00 3.44 30.95 3.55
597 618 6.406093 TGAAAATTGTCAACTTTGCAACAG 57.594 33.333 0.00 2.74 30.95 3.16
599 620 7.002816 TCATGAAAATTGTCAACTTTGCAAC 57.997 32.000 1.55 0.00 30.95 4.17
600 621 7.040494 TCTCATGAAAATTGTCAACTTTGCAA 58.960 30.769 1.55 0.00 0.00 4.08
602 623 7.359765 CCATCTCATGAAAATTGTCAACTTTGC 60.360 37.037 1.55 0.00 0.00 3.68
604 625 7.729116 ACCATCTCATGAAAATTGTCAACTTT 58.271 30.769 1.55 0.00 0.00 2.66
611 633 5.776716 ACCTGAACCATCTCATGAAAATTGT 59.223 36.000 0.00 0.00 0.00 2.71
643 665 5.334569 GCCGTAAATGCAGAAGTCTTTTGTA 60.335 40.000 5.13 0.95 0.00 2.41
657 709 4.622701 ATGAAGAAGAAGCCGTAAATGC 57.377 40.909 0.00 0.00 0.00 3.56
662 714 5.168569 CAACACTATGAAGAAGAAGCCGTA 58.831 41.667 0.00 0.00 0.00 4.02
675 727 0.249120 CGGCTGGACCAACACTATGA 59.751 55.000 0.00 0.00 39.03 2.15
677 729 0.981183 TTCGGCTGGACCAACACTAT 59.019 50.000 0.00 0.00 39.03 2.12
678 730 0.034337 GTTCGGCTGGACCAACACTA 59.966 55.000 0.00 0.00 39.03 2.74
679 731 1.227853 GTTCGGCTGGACCAACACT 60.228 57.895 0.00 0.00 39.03 3.55
688 740 0.676466 TGGTGCTAATGTTCGGCTGG 60.676 55.000 0.00 0.00 0.00 4.85
703 755 2.349590 TGCGATTGAGAAGTCATGGTG 58.650 47.619 0.00 0.00 30.85 4.17
706 758 8.598924 GGTATTATATGCGATTGAGAAGTCATG 58.401 37.037 0.00 0.00 30.85 3.07
722 774 8.551205 GCCGACATGACATTATGGTATTATATG 58.449 37.037 0.00 0.00 32.32 1.78
724 776 7.547722 GTGCCGACATGACATTATGGTATTATA 59.452 37.037 0.00 0.00 32.32 0.98
726 778 5.699001 GTGCCGACATGACATTATGGTATTA 59.301 40.000 0.00 0.00 32.32 0.98
727 779 4.515191 GTGCCGACATGACATTATGGTATT 59.485 41.667 0.00 0.00 32.32 1.89
729 781 3.462982 GTGCCGACATGACATTATGGTA 58.537 45.455 0.00 0.00 32.32 3.25
730 782 2.288666 GTGCCGACATGACATTATGGT 58.711 47.619 0.00 0.00 32.32 3.55
731 783 1.603802 GGTGCCGACATGACATTATGG 59.396 52.381 0.00 0.00 32.32 2.74
732 784 1.261354 CGGTGCCGACATGACATTATG 59.739 52.381 4.35 0.00 42.83 1.90
733 785 1.138069 TCGGTGCCGACATGACATTAT 59.862 47.619 9.48 0.00 44.01 1.28
734 786 0.533032 TCGGTGCCGACATGACATTA 59.467 50.000 9.48 0.00 44.01 1.90
744 796 1.561717 CGTTTCATTGTCGGTGCCGA 61.562 55.000 9.48 9.48 46.87 5.54
748 800 1.130373 CCCATCGTTTCATTGTCGGTG 59.870 52.381 0.00 0.00 35.79 4.94
749 801 1.448985 CCCATCGTTTCATTGTCGGT 58.551 50.000 0.00 0.00 0.00 4.69
750 802 0.732571 CCCCATCGTTTCATTGTCGG 59.267 55.000 0.00 0.00 0.00 4.79
751 803 1.396996 GTCCCCATCGTTTCATTGTCG 59.603 52.381 0.00 0.00 0.00 4.35
771 823 1.815421 ATAAGCTGAAGCCGCACGG 60.815 57.895 4.30 4.30 43.38 4.94
869 927 8.462016 GCAATAGGCCTATGGATTTGTATAAAG 58.538 37.037 28.68 1.98 36.11 1.85
884 942 2.761767 TGAACGTGTAGCAATAGGCCTA 59.238 45.455 16.60 16.60 46.50 3.93
1055 1140 0.175989 GAGACGGATGAACTCACCCC 59.824 60.000 0.00 0.00 0.00 4.95
1059 1144 1.474478 GAGCAGAGACGGATGAACTCA 59.526 52.381 0.00 0.00 33.69 3.41
1086 1171 2.688666 AGGGCATCCTTGAGGCGA 60.689 61.111 0.00 0.00 41.56 5.54
1137 1222 1.988406 GTGGGCGAAGAGGGTAGGT 60.988 63.158 0.00 0.00 0.00 3.08
1322 1407 1.068474 GTTCCAGGACATGACGTTCG 58.932 55.000 0.00 0.00 0.00 3.95
1353 1438 1.001068 TCGCCGTTCTTGATGTAACCA 59.999 47.619 0.00 0.00 0.00 3.67
1412 1497 1.296392 CAGGTGGCGACATTCCTCA 59.704 57.895 0.00 0.00 46.14 3.86
1466 1551 2.362369 CCCAGGCTGTCCTCGTCAT 61.362 63.158 14.43 0.00 41.93 3.06
1563 1648 3.023119 TCCAGAGACAAGATCAGAGAGC 58.977 50.000 0.00 0.00 0.00 4.09
1569 1654 0.532573 GGCGTCCAGAGACAAGATCA 59.467 55.000 0.00 0.00 43.73 2.92
1606 1691 0.914644 ATGTCCATCCCACACCTCAG 59.085 55.000 0.00 0.00 0.00 3.35
1641 1726 0.250467 ACATGTGAGCCAGCGAGTTT 60.250 50.000 0.00 0.00 0.00 2.66
1680 1765 3.302347 AACGGCCTCTCCTTCTGCG 62.302 63.158 0.00 0.00 0.00 5.18
1794 1879 2.025981 CCCAACACCTCTCATCATGGAA 60.026 50.000 0.00 0.00 0.00 3.53
1810 1895 0.179045 ACATCAGCCGCTATCCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
1816 1901 0.179073 GTGACCACATCAGCCGCTAT 60.179 55.000 0.00 0.00 38.28 2.97
1827 1912 5.394224 TGATACTAACGAATGTGACCACA 57.606 39.130 5.22 5.22 46.44 4.17
1848 1933 4.676196 GCCAAATCTGAGCAACAGGTAATG 60.676 45.833 10.23 6.89 45.76 1.90
1899 1984 0.729116 CAGCCTTGATAACCTGTGCG 59.271 55.000 0.00 0.00 0.00 5.34
1974 2059 1.811266 CGAGTCACCCAAGCATCCG 60.811 63.158 0.00 0.00 0.00 4.18
2626 2711 6.096001 GCCATCATTTCTTCCAAGTACTCATT 59.904 38.462 0.00 0.00 0.00 2.57
2769 2854 4.534103 ACTCCTTCAGGTAAGCTCAGAAAT 59.466 41.667 0.00 0.00 36.34 2.17
2953 3038 4.342862 AGATACACACAGTTGAGTGCTT 57.657 40.909 9.18 0.00 43.23 3.91
2982 3067 0.960364 GATCTTGTTCCCCGCAGCAA 60.960 55.000 0.00 0.00 0.00 3.91
2988 3073 4.939052 AGTATACAGATCTTGTTCCCCG 57.061 45.455 5.50 0.00 41.29 5.73
3190 3686 9.288576 CCATCACTTATAGAAGGCAATGATTTA 57.711 33.333 1.59 0.00 36.95 1.40
3297 4044 9.136323 AGAAAACCAAATCTTGTATTTCAGAGT 57.864 29.630 12.64 0.00 36.55 3.24
3299 4046 9.354673 AGAGAAAACCAAATCTTGTATTTCAGA 57.645 29.630 12.64 0.00 36.55 3.27
3445 4197 0.842467 AAGGACCAGAACCTCCAGGG 60.842 60.000 0.00 0.00 40.27 4.45
3459 4211 4.142271 CCACTGTCATACTCTCAGAAGGAC 60.142 50.000 0.00 0.00 33.49 3.85
3472 4224 4.679639 GCACCGATAGTTTCCACTGTCATA 60.680 45.833 0.85 0.00 40.38 2.15
3481 4233 6.854496 TGTATAATTGCACCGATAGTTTCC 57.146 37.500 0.00 0.00 0.00 3.13
3504 4256 1.747355 GCTGCACTATTGTTGCTCCAT 59.253 47.619 0.00 0.00 0.00 3.41
3559 4311 7.407393 TTCCAATCAGAATTATTGCATGACA 57.593 32.000 0.00 0.00 33.80 3.58
3850 4602 3.823304 GAGCAACAAGAGGGAACAGAAAT 59.177 43.478 0.00 0.00 0.00 2.17
3969 4723 0.179032 TGCTTCTTTCAACGAGCCCA 60.179 50.000 0.00 0.00 34.30 5.36
4132 4886 2.955342 ATTGTGCCAGGCCAAAAATT 57.045 40.000 16.53 1.34 0.00 1.82
4154 4908 0.393402 GTCCCGGCCCTTTTATTCGT 60.393 55.000 0.00 0.00 0.00 3.85
4300 6273 6.993786 TTTTTAGGTTTGAAGGCCAAAAAG 57.006 33.333 5.01 0.00 45.40 2.27
4361 6334 1.036707 CCGGCCTTTGTTCCTTTTGA 58.963 50.000 0.00 0.00 0.00 2.69
4367 6343 2.114411 TGGACCGGCCTTTGTTCC 59.886 61.111 14.76 7.21 37.63 3.62


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

AutoCloner maintained by Alex Coulton.