Multiple sequence alignment - TraesCS2B01G172000

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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 TraesCS2B01G172000 chr2B 100.000 2772 0 0 1 2772 146455171 146452400 0.000000e+00 5120
1 TraesCS2B01G172000 chr2D 96.242 1996 26 10 781 2772 94331228 94329278 0.000000e+00 3225
2 TraesCS2B01G172000 chr2D 97.189 676 12 4 1 673 94331892 94331221 0.000000e+00 1136
3 TraesCS2B01G172000 chr2D 97.541 122 2 1 662 783 13599774 13599654 1.010000e-49 207
4 TraesCS2B01G172000 chr2D 97.521 121 2 1 662 782 490824498 490824379 3.620000e-49 206
5 TraesCS2B01G172000 chr2D 93.893 131 8 0 659 789 95519665 95519535 6.060000e-47 198
6 TraesCS2B01G172000 chr2D 95.200 125 6 0 666 790 489410071 489410195 6.060000e-47 198
7 TraesCS2B01G172000 chr2D 93.798 129 8 0 663 791 460869570 460869442 7.830000e-46 195
8 TraesCS2B01G172000 chr2A 94.602 1834 62 10 782 2610 92330818 92329017 0.000000e+00 2804
9 TraesCS2B01G172000 chr2A 93.103 667 42 3 1 667 92331488 92330826 0.000000e+00 974
10 TraesCS2B01G172000 chr2A 91.716 169 10 1 2608 2772 92328684 92328516 5.970000e-57 231
11 TraesCS2B01G172000 chr1B 94.891 137 4 2 647 783 613245913 613246046 7.780000e-51 211
12 TraesCS2B01G172000 chr3B 95.200 125 6 0 662 786 475817009 475816885 6.060000e-47 198
13 TraesCS2B01G172000 chr7D 92.593 135 10 0 663 797 120249287 120249153 7.830000e-46 195
14 TraesCS2B01G172000 chr6B 92.593 135 8 2 658 792 343032973 343032841 2.820000e-45 193


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 TraesCS2B01G172000 chr2B 146452400 146455171 2771 True 5120.000000 5120 100.000000 1 2772 1 chr2B.!!$R1 2771
1 TraesCS2B01G172000 chr2D 94329278 94331892 2614 True 2180.500000 3225 96.715500 1 2772 2 chr2D.!!$R5 2771
2 TraesCS2B01G172000 chr2A 92328516 92331488 2972 True 1336.333333 2804 93.140333 1 2772 3 chr2A.!!$R1 2771

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
684 688 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 2506 0.108945 GGAGCAGGCATTCAACAAGC 60.109 55.0 0.0 0.0 0.0 4.01 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
98 99 2.949644 AGTAACTTTGCTCGCCACTTTT 59.050 40.909 0.00 0.00 0.00 2.27
241 242 3.519510 TCAATTGGTGGTTCCTCTAGGAG 59.480 47.826 5.42 0.00 46.36 3.69
606 610 2.325583 TTGTGATTCCCTGATACCGC 57.674 50.000 0.00 0.00 0.00 5.68
644 648 5.514204 TCGTAGCGCTAGAAGTGTATTTTTC 59.486 40.000 19.48 0.00 0.00 2.29
665 669 5.909621 TCACCTAGCAACGACTAAATACT 57.090 39.130 0.00 0.00 0.00 2.12
666 670 7.395190 TTCACCTAGCAACGACTAAATACTA 57.605 36.000 0.00 0.00 0.00 1.82
667 671 6.789262 TCACCTAGCAACGACTAAATACTAC 58.211 40.000 0.00 0.00 0.00 2.73
668 672 6.600822 TCACCTAGCAACGACTAAATACTACT 59.399 38.462 0.00 0.00 0.00 2.57
669 673 6.911511 CACCTAGCAACGACTAAATACTACTC 59.088 42.308 0.00 0.00 0.00 2.59
670 674 6.039159 ACCTAGCAACGACTAAATACTACTCC 59.961 42.308 0.00 0.00 0.00 3.85
671 675 5.259832 AGCAACGACTAAATACTACTCCC 57.740 43.478 0.00 0.00 0.00 4.30
672 676 4.954826 AGCAACGACTAAATACTACTCCCT 59.045 41.667 0.00 0.00 0.00 4.20
673 677 5.067544 AGCAACGACTAAATACTACTCCCTC 59.932 44.000 0.00 0.00 0.00 4.30
674 678 5.735638 GCAACGACTAAATACTACTCCCTCC 60.736 48.000 0.00 0.00 0.00 4.30
675 679 4.133078 ACGACTAAATACTACTCCCTCCG 58.867 47.826 0.00 0.00 0.00 4.63
676 680 4.133078 CGACTAAATACTACTCCCTCCGT 58.867 47.826 0.00 0.00 0.00 4.69
677 681 4.213059 CGACTAAATACTACTCCCTCCGTC 59.787 50.000 0.00 0.00 0.00 4.79
678 682 4.468713 ACTAAATACTACTCCCTCCGTCC 58.531 47.826 0.00 0.00 0.00 4.79
679 683 1.978454 AATACTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
680 684 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
681 685 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
682 686 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
683 687 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
684 688 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
685 689 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
686 690 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
687 691 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
688 692 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
689 693 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
690 694 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
691 695 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
692 696 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
693 697 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
694 698 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
695 699 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
696 700 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
697 701 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
698 702 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
699 703 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
700 704 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
701 705 3.877508 GGAAATACTTGTCGGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
702 706 4.383770 GGAAATACTTGTCGGAGGAATGGA 60.384 45.833 0.00 0.00 0.00 3.41
703 707 5.368989 GAAATACTTGTCGGAGGAATGGAT 58.631 41.667 0.00 0.00 0.00 3.41
704 708 2.698855 ACTTGTCGGAGGAATGGATG 57.301 50.000 0.00 0.00 0.00 3.51
705 709 1.909302 ACTTGTCGGAGGAATGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
706 710 3.104512 ACTTGTCGGAGGAATGGATGTA 58.895 45.455 0.00 0.00 0.00 2.29
707 711 3.711704 ACTTGTCGGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
708 712 4.202264 ACTTGTCGGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
709 713 3.576861 TGTCGGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 0.00 1.98
710 714 4.736473 TGTCGGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 0.00 1.98
711 715 4.767409 TGTCGGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 0.00 2.43
712 716 5.010933 GTCGGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
713 717 5.654650 GTCGGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
714 718 5.654209 TCGGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
715 719 5.420421 CGGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
716 720 6.603599 CGGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
717 721 7.286546 CGGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
718 722 8.986991 GGAGGAATGGATGTATCTAGATGTATT 58.013 37.037 15.79 6.57 0.00 1.89
747 751 9.407380 AGTTCTACATACATCCATTTTTATGCA 57.593 29.630 0.00 0.00 0.00 3.96
753 757 9.754382 ACATACATCCATTTTTATGCATTTCTC 57.246 29.630 3.54 0.00 0.00 2.87
754 758 9.199982 CATACATCCATTTTTATGCATTTCTCC 57.800 33.333 3.54 0.00 0.00 3.71
755 759 6.275335 ACATCCATTTTTATGCATTTCTCCG 58.725 36.000 3.54 0.00 0.00 4.63
756 760 6.096705 ACATCCATTTTTATGCATTTCTCCGA 59.903 34.615 3.54 0.00 0.00 4.55
757 761 5.890334 TCCATTTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
758 762 5.417266 TCCATTTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
759 763 6.071672 TCCATTTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
760 764 6.254157 CCATTTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
761 765 6.567687 TTTTTATGCATTTCTCCGACAAGA 57.432 33.333 3.54 0.00 0.00 3.02
762 766 6.567687 TTTTATGCATTTCTCCGACAAGAA 57.432 33.333 3.54 0.00 33.50 2.52
763 767 6.757897 TTTATGCATTTCTCCGACAAGAAT 57.242 33.333 3.54 0.00 35.30 2.40
764 768 6.757897 TTATGCATTTCTCCGACAAGAATT 57.242 33.333 3.54 0.00 35.30 2.17
765 769 5.649782 ATGCATTTCTCCGACAAGAATTT 57.350 34.783 0.00 0.00 35.30 1.82
766 770 5.046910 TGCATTTCTCCGACAAGAATTTC 57.953 39.130 0.00 0.00 35.30 2.17
767 771 4.761739 TGCATTTCTCCGACAAGAATTTCT 59.238 37.500 0.00 0.00 35.30 2.52
768 772 5.091431 GCATTTCTCCGACAAGAATTTCTG 58.909 41.667 0.00 0.00 35.30 3.02
769 773 5.634896 CATTTCTCCGACAAGAATTTCTGG 58.365 41.667 0.00 0.00 35.30 3.86
770 774 4.617253 TTCTCCGACAAGAATTTCTGGA 57.383 40.909 7.82 5.56 30.38 3.86
771 775 3.926616 TCTCCGACAAGAATTTCTGGAC 58.073 45.455 7.82 0.68 0.00 4.02
772 776 2.668457 CTCCGACAAGAATTTCTGGACG 59.332 50.000 15.76 15.76 35.81 4.79
773 777 1.732259 CCGACAAGAATTTCTGGACGG 59.268 52.381 23.69 23.69 45.94 4.79
774 778 2.683968 CGACAAGAATTTCTGGACGGA 58.316 47.619 15.14 0.00 33.18 4.69
775 779 2.668457 CGACAAGAATTTCTGGACGGAG 59.332 50.000 15.14 0.00 33.18 4.63
776 780 3.003480 GACAAGAATTTCTGGACGGAGG 58.997 50.000 7.82 0.00 0.00 4.30
777 781 2.290323 ACAAGAATTTCTGGACGGAGGG 60.290 50.000 7.82 0.00 0.00 4.30
778 782 1.952621 AGAATTTCTGGACGGAGGGA 58.047 50.000 0.00 0.00 0.00 4.20
779 783 1.834263 AGAATTTCTGGACGGAGGGAG 59.166 52.381 0.00 0.00 0.00 4.30
791 803 5.082425 GGACGGAGGGAGTATTTCCTTATA 58.918 45.833 0.00 0.00 45.98 0.98
884 896 6.838198 TTGCGTCATCACTAACCAATATAC 57.162 37.500 0.00 0.00 0.00 1.47
1125 1139 2.446036 GCCTCCTACCCCGACCAT 60.446 66.667 0.00 0.00 0.00 3.55
1874 1888 2.017049 GCGATGGGCTTGTCAATTAGT 58.983 47.619 0.00 0.00 39.11 2.24
1986 2000 3.008375 ACAGTTTTCTAGCTGGCTCATCA 59.992 43.478 0.00 0.00 37.07 3.07
1987 2001 4.197750 CAGTTTTCTAGCTGGCTCATCAT 58.802 43.478 0.00 0.00 0.00 2.45
1988 2002 4.035324 CAGTTTTCTAGCTGGCTCATCATG 59.965 45.833 0.00 0.00 0.00 3.07
1989 2003 2.251409 TTCTAGCTGGCTCATCATGC 57.749 50.000 0.00 0.00 0.00 4.06
1990 2004 1.125633 TCTAGCTGGCTCATCATGCA 58.874 50.000 0.00 0.00 0.00 3.96
1991 2005 1.070289 TCTAGCTGGCTCATCATGCAG 59.930 52.381 0.00 0.00 0.00 4.41
1992 2006 0.835276 TAGCTGGCTCATCATGCAGT 59.165 50.000 0.00 0.00 0.00 4.40
1993 2007 0.748367 AGCTGGCTCATCATGCAGTG 60.748 55.000 0.00 0.00 0.00 3.66
1994 2008 1.030488 GCTGGCTCATCATGCAGTGT 61.030 55.000 0.00 0.00 0.00 3.55
1995 2009 1.744798 GCTGGCTCATCATGCAGTGTA 60.745 52.381 0.00 0.00 0.00 2.90
1996 2010 2.847441 CTGGCTCATCATGCAGTGTAT 58.153 47.619 0.00 0.00 0.00 2.29
1997 2011 3.211865 CTGGCTCATCATGCAGTGTATT 58.788 45.455 0.00 0.00 0.00 1.89
1998 2012 3.623703 TGGCTCATCATGCAGTGTATTT 58.376 40.909 0.00 0.00 0.00 1.40
2051 2079 0.248743 TTCGTGAGCGTCGTTCACTT 60.249 50.000 30.85 0.00 40.67 3.16
2052 2080 0.248743 TCGTGAGCGTCGTTCACTTT 60.249 50.000 30.85 0.00 40.67 2.66
2191 2220 9.780413 GTTTAGAATCTGATCATTTTCCAACTC 57.220 33.333 11.97 1.92 0.00 3.01
2239 2270 5.191426 AGATGAAAGAGCATGCTTATGTGT 58.809 37.500 23.61 7.45 0.00 3.72
2320 2351 1.537202 GGTGAGAACATCTGTTGTGGC 59.463 52.381 0.00 0.00 38.99 5.01
2323 2354 0.534877 AGAACATCTGTTGTGGCGCA 60.535 50.000 10.83 0.00 38.99 6.09
2417 2448 8.479313 TCTAATGACACTGATACAATGACAAC 57.521 34.615 0.00 0.00 0.00 3.32
2418 2449 8.093927 TCTAATGACACTGATACAATGACAACA 58.906 33.333 0.00 0.00 0.00 3.33
2424 2455 6.128553 ACACTGATACAATGACAACAATCGTC 60.129 38.462 0.00 0.00 0.00 4.20
2459 2490 0.106519 ACTTCCTGCACCTGCTTGTT 60.107 50.000 0.00 0.00 42.66 2.83
2460 2491 0.313043 CTTCCTGCACCTGCTTGTTG 59.687 55.000 0.00 0.00 42.66 3.33
2461 2492 0.106769 TTCCTGCACCTGCTTGTTGA 60.107 50.000 0.00 0.00 42.66 3.18
2462 2493 0.106769 TCCTGCACCTGCTTGTTGAA 60.107 50.000 0.00 0.00 42.66 2.69
2463 2494 0.963962 CCTGCACCTGCTTGTTGAAT 59.036 50.000 0.00 0.00 42.66 2.57
2464 2495 1.336517 CCTGCACCTGCTTGTTGAATG 60.337 52.381 0.00 0.00 42.66 2.67
2465 2496 0.032403 TGCACCTGCTTGTTGAATGC 59.968 50.000 0.00 0.00 42.66 3.56
2466 2497 0.668401 GCACCTGCTTGTTGAATGCC 60.668 55.000 0.00 0.00 38.21 4.40
2467 2498 0.963962 CACCTGCTTGTTGAATGCCT 59.036 50.000 0.00 0.00 0.00 4.75
2468 2499 0.963962 ACCTGCTTGTTGAATGCCTG 59.036 50.000 0.00 0.00 0.00 4.85
2469 2500 0.389426 CCTGCTTGTTGAATGCCTGC 60.389 55.000 0.00 0.00 0.00 4.85
2470 2501 0.601558 CTGCTTGTTGAATGCCTGCT 59.398 50.000 0.00 0.00 0.00 4.24
2471 2502 0.599558 TGCTTGTTGAATGCCTGCTC 59.400 50.000 0.00 0.00 0.00 4.26
2472 2503 0.108945 GCTTGTTGAATGCCTGCTCC 60.109 55.000 0.00 0.00 0.00 4.70
2473 2504 1.250328 CTTGTTGAATGCCTGCTCCA 58.750 50.000 0.00 0.00 0.00 3.86
2474 2505 1.614903 CTTGTTGAATGCCTGCTCCAA 59.385 47.619 0.00 0.00 0.00 3.53
2475 2506 1.250328 TGTTGAATGCCTGCTCCAAG 58.750 50.000 0.00 0.00 0.00 3.61
2476 2507 0.108945 GTTGAATGCCTGCTCCAAGC 60.109 55.000 0.00 0.00 42.82 4.01
2477 2508 0.251474 TTGAATGCCTGCTCCAAGCT 60.251 50.000 0.11 0.00 42.97 3.74
2478 2509 0.251474 TGAATGCCTGCTCCAAGCTT 60.251 50.000 0.00 0.00 42.97 3.74
2479 2510 0.172803 GAATGCCTGCTCCAAGCTTG 59.827 55.000 19.93 19.93 42.97 4.01
2480 2511 0.541296 AATGCCTGCTCCAAGCTTGT 60.541 50.000 24.35 0.00 42.97 3.16
2562 2593 4.618927 GCTGCCTGTGCTTCATTTCATTAA 60.619 41.667 0.00 0.00 38.71 1.40
2649 3015 1.619704 GGGGGCAGAAGCTATTTTGGT 60.620 52.381 0.00 0.00 41.70 3.67
2653 3019 3.367395 GGGCAGAAGCTATTTTGGTCAAC 60.367 47.826 0.00 0.00 41.70 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.758528 GGCTTAAGAGTAGACGTTCTGAATTAA 59.241 37.037 6.67 0.00 0.00 1.40
98 99 5.580297 GGCTTGATGACAACAAACAAGAAAA 59.420 36.000 17.13 0.00 41.71 2.29
110 111 3.667087 GCCACGGCTTGATGACAA 58.333 55.556 0.00 0.00 38.26 3.18
241 242 3.494251 CAGCCACAAACCAACAATAAAGC 59.506 43.478 0.00 0.00 0.00 3.51
606 610 6.946229 AGCGCTACGAAATTGTATATTAGG 57.054 37.500 8.99 0.00 0.00 2.69
644 648 6.793349 AGTAGTATTTAGTCGTTGCTAGGTG 58.207 40.000 0.00 0.00 0.00 4.00
665 669 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
666 670 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
667 671 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
668 672 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
669 673 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
670 674 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
671 675 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
672 676 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
673 677 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
674 678 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
675 679 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
676 680 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
677 681 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
678 682 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
679 683 3.877508 CCATTCCTCCGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
680 684 4.766375 TCCATTCCTCCGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
681 685 4.837093 TCCATTCCTCCGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
682 686 4.164221 ACATCCATTCCTCCGACAAGTATT 59.836 41.667 0.00 0.00 0.00 1.89
683 687 3.711704 ACATCCATTCCTCCGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
684 688 3.104512 ACATCCATTCCTCCGACAAGTA 58.895 45.455 0.00 0.00 0.00 2.24
685 689 1.909302 ACATCCATTCCTCCGACAAGT 59.091 47.619 0.00 0.00 0.00 3.16
686 690 2.698855 ACATCCATTCCTCCGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
687 691 3.967326 AGATACATCCATTCCTCCGACAA 59.033 43.478 0.00 0.00 0.00 3.18
688 692 3.576861 AGATACATCCATTCCTCCGACA 58.423 45.455 0.00 0.00 0.00 4.35
689 693 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
690 694 5.256806 TCTAGATACATCCATTCCTCCGA 57.743 43.478 0.00 0.00 0.00 4.55
691 695 5.420421 ACATCTAGATACATCCATTCCTCCG 59.580 44.000 4.54 0.00 0.00 4.63
692 696 6.865834 ACATCTAGATACATCCATTCCTCC 57.134 41.667 4.54 0.00 0.00 4.30
721 725 9.407380 TGCATAAAAATGGATGTATGTAGAACT 57.593 29.630 0.00 0.00 0.00 3.01
727 731 9.754382 GAGAAATGCATAAAAATGGATGTATGT 57.246 29.630 0.00 0.00 32.82 2.29
728 732 9.199982 GGAGAAATGCATAAAAATGGATGTATG 57.800 33.333 0.00 0.00 32.82 2.39
729 733 8.084073 CGGAGAAATGCATAAAAATGGATGTAT 58.916 33.333 0.00 0.00 32.82 2.29
730 734 7.284261 TCGGAGAAATGCATAAAAATGGATGTA 59.716 33.333 0.00 0.00 32.82 2.29
731 735 6.096705 TCGGAGAAATGCATAAAAATGGATGT 59.903 34.615 0.00 0.00 32.82 3.06
732 736 6.418819 GTCGGAGAAATGCATAAAAATGGATG 59.581 38.462 0.00 0.00 39.69 3.51
733 737 6.096705 TGTCGGAGAAATGCATAAAAATGGAT 59.903 34.615 0.00 0.00 39.69 3.41
734 738 5.417266 TGTCGGAGAAATGCATAAAAATGGA 59.583 36.000 0.00 0.00 39.69 3.41
735 739 5.649557 TGTCGGAGAAATGCATAAAAATGG 58.350 37.500 0.00 0.00 39.69 3.16
736 740 7.028962 TCTTGTCGGAGAAATGCATAAAAATG 58.971 34.615 0.00 0.00 39.69 2.32
737 741 7.156876 TCTTGTCGGAGAAATGCATAAAAAT 57.843 32.000 0.00 0.00 39.69 1.82
738 742 6.567687 TCTTGTCGGAGAAATGCATAAAAA 57.432 33.333 0.00 0.00 39.69 1.94
739 743 6.567687 TTCTTGTCGGAGAAATGCATAAAA 57.432 33.333 0.00 0.00 39.69 1.52
740 744 6.757897 ATTCTTGTCGGAGAAATGCATAAA 57.242 33.333 0.00 0.00 39.69 1.40
741 745 6.757897 AATTCTTGTCGGAGAAATGCATAA 57.242 33.333 0.00 0.00 39.69 1.90
742 746 6.599244 AGAAATTCTTGTCGGAGAAATGCATA 59.401 34.615 0.00 0.00 39.69 3.14
743 747 5.416952 AGAAATTCTTGTCGGAGAAATGCAT 59.583 36.000 0.00 0.00 39.69 3.96
744 748 4.761739 AGAAATTCTTGTCGGAGAAATGCA 59.238 37.500 0.00 0.00 39.69 3.96
745 749 5.091431 CAGAAATTCTTGTCGGAGAAATGC 58.909 41.667 0.00 0.00 39.69 3.56
746 750 5.412594 TCCAGAAATTCTTGTCGGAGAAATG 59.587 40.000 0.00 0.81 39.69 2.32
747 751 5.412904 GTCCAGAAATTCTTGTCGGAGAAAT 59.587 40.000 0.63 0.00 39.69 2.17
748 752 4.755123 GTCCAGAAATTCTTGTCGGAGAAA 59.245 41.667 0.63 0.00 39.69 2.52
749 753 4.315803 GTCCAGAAATTCTTGTCGGAGAA 58.684 43.478 0.63 0.54 39.69 2.87
750 754 3.614150 CGTCCAGAAATTCTTGTCGGAGA 60.614 47.826 5.98 0.00 0.00 3.71
751 755 2.668457 CGTCCAGAAATTCTTGTCGGAG 59.332 50.000 5.98 0.00 0.00 4.63
752 756 2.611971 CCGTCCAGAAATTCTTGTCGGA 60.612 50.000 21.47 10.45 38.03 4.55
753 757 1.732259 CCGTCCAGAAATTCTTGTCGG 59.268 52.381 15.43 15.43 0.00 4.79
754 758 2.668457 CTCCGTCCAGAAATTCTTGTCG 59.332 50.000 6.71 6.71 0.00 4.35
755 759 3.003480 CCTCCGTCCAGAAATTCTTGTC 58.997 50.000 0.00 0.00 0.00 3.18
756 760 2.290323 CCCTCCGTCCAGAAATTCTTGT 60.290 50.000 0.00 0.00 0.00 3.16
757 761 2.027192 TCCCTCCGTCCAGAAATTCTTG 60.027 50.000 0.00 0.00 0.00 3.02
758 762 2.237392 CTCCCTCCGTCCAGAAATTCTT 59.763 50.000 0.00 0.00 0.00 2.52
759 763 1.834263 CTCCCTCCGTCCAGAAATTCT 59.166 52.381 0.00 0.00 0.00 2.40
760 764 1.555533 ACTCCCTCCGTCCAGAAATTC 59.444 52.381 0.00 0.00 0.00 2.17
761 765 1.657804 ACTCCCTCCGTCCAGAAATT 58.342 50.000 0.00 0.00 0.00 1.82
762 766 2.544844 TACTCCCTCCGTCCAGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
763 767 2.544844 ATACTCCCTCCGTCCAGAAA 57.455 50.000 0.00 0.00 0.00 2.52
764 768 2.544844 AATACTCCCTCCGTCCAGAA 57.455 50.000 0.00 0.00 0.00 3.02
765 769 2.385803 GAAATACTCCCTCCGTCCAGA 58.614 52.381 0.00 0.00 0.00 3.86
766 770 1.413077 GGAAATACTCCCTCCGTCCAG 59.587 57.143 0.00 0.00 38.44 3.86
767 771 1.007963 AGGAAATACTCCCTCCGTCCA 59.992 52.381 0.00 0.00 46.81 4.02
768 772 1.790818 AGGAAATACTCCCTCCGTCC 58.209 55.000 0.00 0.00 46.81 4.79
769 773 6.854091 ATATAAGGAAATACTCCCTCCGTC 57.146 41.667 0.00 0.00 46.81 4.79
770 774 7.179872 GGTAATATAAGGAAATACTCCCTCCGT 59.820 40.741 0.00 0.00 46.81 4.69
771 775 7.554211 GGTAATATAAGGAAATACTCCCTCCG 58.446 42.308 0.00 0.00 46.81 4.63
772 776 7.179872 ACGGTAATATAAGGAAATACTCCCTCC 59.820 40.741 0.00 0.00 46.81 4.30
773 777 8.131847 ACGGTAATATAAGGAAATACTCCCTC 57.868 38.462 0.00 0.00 46.81 4.30
774 778 8.502047 AACGGTAATATAAGGAAATACTCCCT 57.498 34.615 0.00 0.00 46.81 4.20
775 779 9.645059 GTAACGGTAATATAAGGAAATACTCCC 57.355 37.037 0.00 0.00 46.81 4.30
791 803 7.380602 GCGTTATGATTCTACTGTAACGGTAAT 59.619 37.037 15.01 0.00 44.43 1.89
870 882 8.491958 AGGAAACCTAAGGTATATTGGTTAGTG 58.508 37.037 0.00 0.00 39.74 2.74
1125 1139 5.550403 AGGAAGGGGAGTTTGATTACTAACA 59.450 40.000 0.00 0.00 35.03 2.41
1874 1888 9.554395 TTTTTCTCATATACACTCAACAAGACA 57.446 29.630 0.00 0.00 0.00 3.41
1986 2000 6.118170 AGCTGATGAGTTAAATACACTGCAT 58.882 36.000 0.00 0.00 0.00 3.96
1987 2001 5.491070 AGCTGATGAGTTAAATACACTGCA 58.509 37.500 0.00 0.00 0.00 4.41
1988 2002 5.814705 AGAGCTGATGAGTTAAATACACTGC 59.185 40.000 0.00 0.00 0.00 4.40
1989 2003 8.812329 GTTAGAGCTGATGAGTTAAATACACTG 58.188 37.037 0.00 0.00 0.00 3.66
1990 2004 7.982354 GGTTAGAGCTGATGAGTTAAATACACT 59.018 37.037 0.00 0.00 0.00 3.55
1991 2005 7.764443 TGGTTAGAGCTGATGAGTTAAATACAC 59.236 37.037 0.00 0.00 0.00 2.90
1992 2006 7.764443 GTGGTTAGAGCTGATGAGTTAAATACA 59.236 37.037 0.00 0.00 0.00 2.29
1993 2007 7.764443 TGTGGTTAGAGCTGATGAGTTAAATAC 59.236 37.037 0.00 0.00 0.00 1.89
1994 2008 7.847096 TGTGGTTAGAGCTGATGAGTTAAATA 58.153 34.615 0.00 0.00 0.00 1.40
1995 2009 6.711277 TGTGGTTAGAGCTGATGAGTTAAAT 58.289 36.000 0.00 0.00 0.00 1.40
1996 2010 6.109156 TGTGGTTAGAGCTGATGAGTTAAA 57.891 37.500 0.00 0.00 0.00 1.52
1997 2011 5.738619 TGTGGTTAGAGCTGATGAGTTAA 57.261 39.130 0.00 0.00 0.00 2.01
1998 2012 5.738619 TTGTGGTTAGAGCTGATGAGTTA 57.261 39.130 0.00 0.00 0.00 2.24
2028 2056 1.465777 TGAACGACGCTCACGAATCTA 59.534 47.619 0.00 0.00 43.93 1.98
2210 2241 9.577110 CATAAGCATGCTCTTTCATCTTTAAAA 57.423 29.630 22.93 0.00 0.00 1.52
2320 2351 1.310933 ATTGCCTGCTTTCTCCTGCG 61.311 55.000 0.00 0.00 0.00 5.18
2417 2448 3.748048 AGACACAGACATTTGGACGATTG 59.252 43.478 0.00 0.00 0.00 2.67
2418 2449 4.008074 AGACACAGACATTTGGACGATT 57.992 40.909 0.00 0.00 0.00 3.34
2424 2455 4.692625 CAGGAAGTAGACACAGACATTTGG 59.307 45.833 0.00 0.00 0.00 3.28
2459 2490 0.251474 AAGCTTGGAGCAGGCATTCA 60.251 50.000 0.00 0.00 45.56 2.57
2460 2491 0.172803 CAAGCTTGGAGCAGGCATTC 59.827 55.000 19.14 0.00 45.56 2.67
2461 2492 0.541296 ACAAGCTTGGAGCAGGCATT 60.541 50.000 29.18 2.15 45.56 3.56
2462 2493 0.541296 AACAAGCTTGGAGCAGGCAT 60.541 50.000 29.18 2.92 45.56 4.40
2463 2494 1.152694 AACAAGCTTGGAGCAGGCA 60.153 52.632 29.18 0.00 45.56 4.75
2464 2495 1.174712 TCAACAAGCTTGGAGCAGGC 61.175 55.000 29.18 0.00 45.56 4.85
2465 2496 1.321474 TTCAACAAGCTTGGAGCAGG 58.679 50.000 29.18 12.08 45.56 4.85
2466 2497 2.925306 GCATTCAACAAGCTTGGAGCAG 60.925 50.000 29.18 15.26 45.56 4.24
2467 2498 1.000060 GCATTCAACAAGCTTGGAGCA 60.000 47.619 29.18 12.67 45.56 4.26
2468 2499 1.670967 GGCATTCAACAAGCTTGGAGC 60.671 52.381 29.18 20.61 42.84 4.70
2469 2500 1.891150 AGGCATTCAACAAGCTTGGAG 59.109 47.619 29.18 20.38 0.00 3.86
2470 2501 1.614903 CAGGCATTCAACAAGCTTGGA 59.385 47.619 29.18 15.56 32.48 3.53
2471 2502 1.938016 GCAGGCATTCAACAAGCTTGG 60.938 52.381 29.18 13.43 36.08 3.61
2472 2503 1.000506 AGCAGGCATTCAACAAGCTTG 59.999 47.619 24.84 24.84 38.26 4.01
2473 2504 1.271656 GAGCAGGCATTCAACAAGCTT 59.728 47.619 0.00 0.00 0.00 3.74
2474 2505 0.886563 GAGCAGGCATTCAACAAGCT 59.113 50.000 0.00 0.00 0.00 3.74
2475 2506 0.108945 GGAGCAGGCATTCAACAAGC 60.109 55.000 0.00 0.00 0.00 4.01
2476 2507 1.250328 TGGAGCAGGCATTCAACAAG 58.750 50.000 0.00 0.00 0.00 3.16
2477 2508 1.546923 CATGGAGCAGGCATTCAACAA 59.453 47.619 0.00 0.00 0.00 2.83
2478 2509 1.179152 CATGGAGCAGGCATTCAACA 58.821 50.000 0.00 0.00 0.00 3.33
2479 2510 1.180029 ACATGGAGCAGGCATTCAAC 58.820 50.000 0.00 0.00 0.00 3.18
2480 2511 1.820519 GAACATGGAGCAGGCATTCAA 59.179 47.619 0.00 0.00 0.00 2.69
2562 2593 5.567037 TGCCAAGCTGGTTGATACTATAT 57.433 39.130 20.26 0.00 40.46 0.86
2649 3015 1.003580 GCAAGAGGTGGATGAGGTTGA 59.996 52.381 0.00 0.00 0.00 3.18
2653 3019 3.473147 CAGCAAGAGGTGGATGAGG 57.527 57.895 0.00 0.00 39.53 3.86


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

AutoCloner maintained by Alex Coulton.