Multiple sequence alignment - TraesCS2A01G059300

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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 TraesCS2A01G059300 chr2A 100.000 3230 0 0 1 3230 25342179 25345408 0.000000e+00 5965.0
1 TraesCS2A01G059300 chr2A 96.262 642 22 2 8 649 25336697 25337336 0.000000e+00 1051.0
2 TraesCS2A01G059300 chr2A 95.122 41 2 0 2300 2340 25344440 25344480 7.480000e-07 65.8
3 TraesCS2A01G059300 chr2A 95.122 41 2 0 2262 2302 25344478 25344518 7.480000e-07 65.8
4 TraesCS2A01G059300 chr2B 94.263 2475 108 14 773 3230 36839064 36841521 0.000000e+00 3753.0
5 TraesCS2A01G059300 chr2B 95.122 41 2 0 2262 2302 36840586 36840626 7.480000e-07 65.8
6 TraesCS2A01G059300 chr2D 94.334 1906 76 15 750 2651 23422663 23420786 0.000000e+00 2892.0
7 TraesCS2A01G059300 chr2D 94.151 530 23 2 2619 3141 23420779 23420251 0.000000e+00 800.0
8 TraesCS2A01G059300 chr2D 98.462 65 1 0 3166 3230 23420252 23420188 7.320000e-22 115.0
9 TraesCS2A01G059300 chr2D 97.222 36 1 0 2267 2302 23421121 23421086 9.680000e-06 62.1
10 TraesCS2A01G059300 chr1A 97.068 648 19 0 2 649 62485832 62486479 0.000000e+00 1092.0
11 TraesCS2A01G059300 chr3A 95.853 651 27 0 2 652 26858714 26858064 0.000000e+00 1053.0
12 TraesCS2A01G059300 chr3A 95.679 648 28 0 2 649 26864177 26863530 0.000000e+00 1042.0
13 TraesCS2A01G059300 chr3A 96.326 626 21 2 25 649 158357391 158358015 0.000000e+00 1027.0
14 TraesCS2A01G059300 chr3A 95.223 649 31 0 1 649 719954751 719955399 0.000000e+00 1027.0
15 TraesCS2A01G059300 chr3A 95.356 646 22 1 4 649 158405337 158405974 0.000000e+00 1020.0
16 TraesCS2A01G059300 chr3A 94.915 649 33 0 2 650 719960228 719960876 0.000000e+00 1016.0
17 TraesCS2A01G059300 chr5A 95.532 649 26 1 2 650 569536906 569537551 0.000000e+00 1035.0
18 TraesCS2A01G059300 chr3D 100.000 28 0 0 974 1001 603746404 603746431 6.000000e-03 52.8


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 TraesCS2A01G059300 chr2A 25342179 25345408 3229 False 2032.200 5965 96.74800 1 3230 3 chr2A.!!$F2 3229
1 TraesCS2A01G059300 chr2A 25336697 25337336 639 False 1051.000 1051 96.26200 8 649 1 chr2A.!!$F1 641
2 TraesCS2A01G059300 chr2B 36839064 36841521 2457 False 1909.400 3753 94.69250 773 3230 2 chr2B.!!$F1 2457
3 TraesCS2A01G059300 chr2D 23420188 23422663 2475 True 967.275 2892 96.04225 750 3230 4 chr2D.!!$R1 2480
4 TraesCS2A01G059300 chr1A 62485832 62486479 647 False 1092.000 1092 97.06800 2 649 1 chr1A.!!$F1 647
5 TraesCS2A01G059300 chr3A 26858064 26858714 650 True 1053.000 1053 95.85300 2 652 1 chr3A.!!$R1 650
6 TraesCS2A01G059300 chr3A 26863530 26864177 647 True 1042.000 1042 95.67900 2 649 1 chr3A.!!$R2 647
7 TraesCS2A01G059300 chr3A 158357391 158358015 624 False 1027.000 1027 96.32600 25 649 1 chr3A.!!$F1 624
8 TraesCS2A01G059300 chr3A 719954751 719955399 648 False 1027.000 1027 95.22300 1 649 1 chr3A.!!$F3 648
9 TraesCS2A01G059300 chr3A 158405337 158405974 637 False 1020.000 1020 95.35600 4 649 1 chr3A.!!$F2 645
10 TraesCS2A01G059300 chr3A 719960228 719960876 648 False 1016.000 1016 94.91500 2 650 1 chr3A.!!$F4 648
11 TraesCS2A01G059300 chr5A 569536906 569537551 645 False 1035.000 1035 95.53200 2 650 1 chr5A.!!$F1 648

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
660 663 0.035820 TTCCAACATCAGGTACGGGC 60.036 55.0 0.0 0.00 0.00 6.13 F
665 668 0.107703 ACATCAGGTACGGGCACATG 60.108 55.0 0.0 0.00 0.00 3.21 F
666 669 0.177836 CATCAGGTACGGGCACATGA 59.822 55.0 0.0 4.34 42.74 3.07 F
667 670 0.178068 ATCAGGTACGGGCACATGAC 59.822 55.0 0.0 0.00 41.52 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1792 0.171231 GAGAACTCCATTTTGCGGGC 59.829 55.000 0.00 0.0 0.00 6.13 R
1980 1998 0.181350 ATTCCTCGGGCAAGGTGATC 59.819 55.000 5.22 0.0 37.69 2.92 R
2076 2094 1.704628 TGCTCAACAGGATCTCCCAAA 59.295 47.619 0.00 0.0 37.41 3.28 R
2524 2550 4.032355 AAACAACACGTTTTAGATGTGCG 58.968 39.130 0.00 0.0 45.79 5.34 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
117 118 3.071023 CAGTGGAGTGAACCCTAACTCAA 59.929 47.826 5.29 0.00 43.81 3.02
128 129 4.899502 ACCCTAACTCAATTCACTCACTG 58.100 43.478 0.00 0.00 0.00 3.66
511 514 5.723672 ACTTATGCTAGCCGTATATGTGT 57.276 39.130 13.29 0.00 30.89 3.72
611 614 4.178540 GCCATGCTTACTGTTTACTCGTA 58.821 43.478 0.00 0.00 0.00 3.43
626 629 9.317936 TGTTTACTCGTAGATAAGTCTAATCGA 57.682 33.333 0.00 0.00 38.62 3.59
652 655 9.643693 AAAAAGTGCTAATATTTCCAACATCAG 57.356 29.630 0.00 0.00 0.00 2.90
653 656 6.949352 AGTGCTAATATTTCCAACATCAGG 57.051 37.500 0.00 0.00 0.00 3.86
654 657 6.426587 AGTGCTAATATTTCCAACATCAGGT 58.573 36.000 0.00 0.00 0.00 4.00
655 658 7.573710 AGTGCTAATATTTCCAACATCAGGTA 58.426 34.615 0.00 0.00 0.00 3.08
656 659 7.499232 AGTGCTAATATTTCCAACATCAGGTAC 59.501 37.037 0.00 0.00 0.00 3.34
657 660 6.481976 TGCTAATATTTCCAACATCAGGTACG 59.518 38.462 0.00 0.00 0.00 3.67
658 661 6.073222 GCTAATATTTCCAACATCAGGTACGG 60.073 42.308 0.00 0.00 0.00 4.02
659 662 2.483014 TTTCCAACATCAGGTACGGG 57.517 50.000 0.00 0.00 0.00 5.28
660 663 0.035820 TTCCAACATCAGGTACGGGC 60.036 55.000 0.00 0.00 0.00 6.13
661 664 1.195442 TCCAACATCAGGTACGGGCA 61.195 55.000 0.00 0.00 0.00 5.36
662 665 1.024579 CCAACATCAGGTACGGGCAC 61.025 60.000 0.00 0.00 0.00 5.01
663 666 0.321210 CAACATCAGGTACGGGCACA 60.321 55.000 0.00 0.00 0.00 4.57
664 667 0.618458 AACATCAGGTACGGGCACAT 59.382 50.000 0.00 0.00 0.00 3.21
665 668 0.107703 ACATCAGGTACGGGCACATG 60.108 55.000 0.00 0.00 0.00 3.21
666 669 0.177836 CATCAGGTACGGGCACATGA 59.822 55.000 0.00 4.34 42.74 3.07
667 670 0.178068 ATCAGGTACGGGCACATGAC 59.822 55.000 0.00 0.00 41.52 3.06
668 671 1.188871 TCAGGTACGGGCACATGACA 61.189 55.000 0.00 0.00 34.53 3.58
669 672 0.321210 CAGGTACGGGCACATGACAA 60.321 55.000 0.00 0.00 32.01 3.18
670 673 0.398696 AGGTACGGGCACATGACAAA 59.601 50.000 0.00 0.00 0.00 2.83
671 674 1.004277 AGGTACGGGCACATGACAAAT 59.996 47.619 0.00 0.00 0.00 2.32
672 675 1.400494 GGTACGGGCACATGACAAATC 59.600 52.381 0.00 0.00 0.00 2.17
673 676 1.062002 GTACGGGCACATGACAAATCG 59.938 52.381 0.00 0.00 0.00 3.34
674 677 0.321210 ACGGGCACATGACAAATCGA 60.321 50.000 0.00 0.00 0.00 3.59
675 678 0.801872 CGGGCACATGACAAATCGAA 59.198 50.000 0.00 0.00 0.00 3.71
676 679 1.465689 CGGGCACATGACAAATCGAAC 60.466 52.381 0.00 0.00 0.00 3.95
677 680 1.539388 GGGCACATGACAAATCGAACA 59.461 47.619 0.00 0.00 0.00 3.18
678 681 2.164219 GGGCACATGACAAATCGAACAT 59.836 45.455 0.00 0.00 0.00 2.71
679 682 3.367292 GGGCACATGACAAATCGAACATT 60.367 43.478 0.00 0.00 0.00 2.71
680 683 4.236935 GGCACATGACAAATCGAACATTT 58.763 39.130 0.00 0.00 0.00 2.32
681 684 4.685628 GGCACATGACAAATCGAACATTTT 59.314 37.500 0.00 0.00 0.00 1.82
682 685 5.177327 GGCACATGACAAATCGAACATTTTT 59.823 36.000 0.00 0.00 0.00 1.94
683 686 6.291385 GCACATGACAAATCGAACATTTTTC 58.709 36.000 0.00 0.00 0.00 2.29
684 687 6.074409 GCACATGACAAATCGAACATTTTTCA 60.074 34.615 0.00 2.33 33.82 2.69
685 688 7.359431 GCACATGACAAATCGAACATTTTTCAT 60.359 33.333 0.00 6.01 38.31 2.57
688 691 7.621832 TGACAAATCGAACATTTTTCATGAC 57.378 32.000 0.00 0.00 0.00 3.06
689 692 7.199078 TGACAAATCGAACATTTTTCATGACA 58.801 30.769 0.00 0.00 0.00 3.58
690 693 7.704047 TGACAAATCGAACATTTTTCATGACAA 59.296 29.630 0.00 0.00 0.00 3.18
691 694 8.064447 ACAAATCGAACATTTTTCATGACAAG 57.936 30.769 0.00 0.00 0.00 3.16
692 695 7.706179 ACAAATCGAACATTTTTCATGACAAGT 59.294 29.630 0.00 0.00 0.00 3.16
693 696 8.542132 CAAATCGAACATTTTTCATGACAAGTT 58.458 29.630 0.00 0.00 0.00 2.66
694 697 7.858052 ATCGAACATTTTTCATGACAAGTTC 57.142 32.000 13.05 13.05 0.00 3.01
695 698 6.790282 TCGAACATTTTTCATGACAAGTTCA 58.210 32.000 18.92 9.27 39.11 3.18
696 699 6.912051 TCGAACATTTTTCATGACAAGTTCAG 59.088 34.615 18.92 13.99 37.77 3.02
697 700 6.692681 CGAACATTTTTCATGACAAGTTCAGT 59.307 34.615 18.92 1.97 37.77 3.41
698 701 7.305590 CGAACATTTTTCATGACAAGTTCAGTG 60.306 37.037 18.92 6.62 37.77 3.66
699 702 7.099266 ACATTTTTCATGACAAGTTCAGTGA 57.901 32.000 0.00 0.00 37.77 3.41
700 703 7.719483 ACATTTTTCATGACAAGTTCAGTGAT 58.281 30.769 0.00 0.00 37.77 3.06
701 704 7.650504 ACATTTTTCATGACAAGTTCAGTGATG 59.349 33.333 0.00 0.00 37.77 3.07
702 705 4.754372 TTCATGACAAGTTCAGTGATGC 57.246 40.909 0.00 0.00 37.77 3.91
703 706 3.742385 TCATGACAAGTTCAGTGATGCA 58.258 40.909 0.00 0.00 37.77 3.96
704 707 4.136051 TCATGACAAGTTCAGTGATGCAA 58.864 39.130 0.00 0.00 37.77 4.08
705 708 4.214758 TCATGACAAGTTCAGTGATGCAAG 59.785 41.667 0.00 0.00 37.77 4.01
706 709 2.880268 TGACAAGTTCAGTGATGCAAGG 59.120 45.455 0.00 0.00 0.00 3.61
707 710 3.141398 GACAAGTTCAGTGATGCAAGGA 58.859 45.455 0.00 0.00 0.00 3.36
708 711 3.755378 GACAAGTTCAGTGATGCAAGGAT 59.245 43.478 0.00 0.00 0.00 3.24
709 712 3.504906 ACAAGTTCAGTGATGCAAGGATG 59.495 43.478 0.00 0.00 0.00 3.51
710 713 3.708403 AGTTCAGTGATGCAAGGATGA 57.292 42.857 0.00 0.00 0.00 2.92
711 714 3.341823 AGTTCAGTGATGCAAGGATGAC 58.658 45.455 0.00 0.00 0.00 3.06
712 715 3.076621 GTTCAGTGATGCAAGGATGACA 58.923 45.455 0.00 0.00 0.00 3.58
713 716 3.421919 TCAGTGATGCAAGGATGACAA 57.578 42.857 0.00 0.00 0.00 3.18
714 717 3.959293 TCAGTGATGCAAGGATGACAAT 58.041 40.909 0.00 0.00 0.00 2.71
715 718 4.338012 TCAGTGATGCAAGGATGACAATT 58.662 39.130 0.00 0.00 0.00 2.32
716 719 4.768448 TCAGTGATGCAAGGATGACAATTT 59.232 37.500 0.00 0.00 0.00 1.82
717 720 5.244402 TCAGTGATGCAAGGATGACAATTTT 59.756 36.000 0.00 0.00 0.00 1.82
718 721 6.433716 TCAGTGATGCAAGGATGACAATTTTA 59.566 34.615 0.00 0.00 0.00 1.52
719 722 6.750501 CAGTGATGCAAGGATGACAATTTTAG 59.249 38.462 0.00 0.00 0.00 1.85
720 723 6.435277 AGTGATGCAAGGATGACAATTTTAGT 59.565 34.615 0.00 0.00 0.00 2.24
721 724 7.039504 AGTGATGCAAGGATGACAATTTTAGTT 60.040 33.333 0.00 0.00 0.00 2.24
722 725 7.062605 GTGATGCAAGGATGACAATTTTAGTTG 59.937 37.037 0.00 0.00 35.25 3.16
723 726 5.782047 TGCAAGGATGACAATTTTAGTTGG 58.218 37.500 0.00 0.00 33.40 3.77
724 727 4.627035 GCAAGGATGACAATTTTAGTTGGC 59.373 41.667 0.00 0.00 37.63 4.52
732 735 7.048629 TGACAATTTTAGTTGGCAAAGATGA 57.951 32.000 0.00 0.00 43.81 2.92
733 736 6.922957 TGACAATTTTAGTTGGCAAAGATGAC 59.077 34.615 0.00 0.00 43.81 3.06
734 737 6.815089 ACAATTTTAGTTGGCAAAGATGACA 58.185 32.000 0.00 0.00 44.97 3.58
785 789 0.813184 CGTCGGGCCAAACTAGAGTA 59.187 55.000 4.39 0.00 0.00 2.59
822 826 4.390048 GCGAGTGGGCCAAAACTA 57.610 55.556 8.40 0.00 0.00 2.24
825 829 0.605319 CGAGTGGGCCAAAACTAGCA 60.605 55.000 8.40 0.00 0.00 3.49
957 969 0.674581 TTCTCTCCGTCGCCGTAGAA 60.675 55.000 0.00 0.00 28.01 2.10
959 971 2.277120 CTCCGTCGCCGTAGAACG 60.277 66.667 0.00 0.00 42.11 3.95
960 972 3.031964 CTCCGTCGCCGTAGAACGT 62.032 63.158 0.00 0.00 40.58 3.99
961 973 1.695893 CTCCGTCGCCGTAGAACGTA 61.696 60.000 0.00 0.00 40.58 3.57
962 974 1.297158 CCGTCGCCGTAGAACGTAG 60.297 63.158 0.00 0.00 40.58 3.51
963 975 1.695893 CCGTCGCCGTAGAACGTAGA 61.696 60.000 0.00 0.00 40.58 2.59
964 976 0.302890 CGTCGCCGTAGAACGTAGAT 59.697 55.000 0.00 0.00 40.58 1.98
965 977 1.655876 CGTCGCCGTAGAACGTAGATC 60.656 57.143 0.00 0.00 40.58 2.75
966 978 0.940126 TCGCCGTAGAACGTAGATCC 59.060 55.000 0.00 0.00 40.58 3.36
967 979 0.659427 CGCCGTAGAACGTAGATCCA 59.341 55.000 0.00 0.00 40.58 3.41
968 980 1.596464 CGCCGTAGAACGTAGATCCAC 60.596 57.143 0.00 0.00 40.58 4.02
969 981 1.268948 GCCGTAGAACGTAGATCCACC 60.269 57.143 0.00 0.00 40.58 4.61
970 982 1.003116 CCGTAGAACGTAGATCCACCG 60.003 57.143 0.00 0.00 40.58 4.94
971 983 1.596464 CGTAGAACGTAGATCCACCGC 60.596 57.143 0.00 0.00 36.74 5.68
972 984 1.674962 GTAGAACGTAGATCCACCGCT 59.325 52.381 0.00 0.00 0.00 5.52
973 985 0.739561 AGAACGTAGATCCACCGCTC 59.260 55.000 0.00 0.00 0.00 5.03
974 986 0.248949 GAACGTAGATCCACCGCTCC 60.249 60.000 0.00 0.00 0.00 4.70
975 987 2.001361 AACGTAGATCCACCGCTCCG 62.001 60.000 0.00 0.00 0.00 4.63
1033 1051 4.477975 CGCTCACCGACGACCTCC 62.478 72.222 0.00 0.00 40.02 4.30
1527 1545 1.092345 GCAACGAGATCTTCCTGGCC 61.092 60.000 0.00 0.00 0.00 5.36
1530 1548 1.045911 ACGAGATCTTCCTGGCCTCC 61.046 60.000 3.32 0.00 0.00 4.30
1613 1631 1.214589 GGAAGCTGGTCGCGTTCTA 59.785 57.895 5.77 0.00 45.59 2.10
1692 1710 4.195334 ATGCGGAGGGTCATGGGC 62.195 66.667 0.00 0.00 0.00 5.36
1809 1827 3.772025 AGTTCTCCATCCTCGACATTTCT 59.228 43.478 0.00 0.00 0.00 2.52
1869 1887 0.542938 TCACCACTCTGGAGTCAGGG 60.543 60.000 10.50 7.68 46.72 4.45
1980 1998 1.285023 GTGGCAGCTGCAGAACAAG 59.715 57.895 37.63 2.29 44.36 3.16
2049 2067 2.951642 TGCATTTGAGGGCTGCTTATAC 59.048 45.455 0.00 0.00 36.84 1.47
2055 2073 7.684187 GCATTTGAGGGCTGCTTATACATAAAA 60.684 37.037 0.00 0.00 33.15 1.52
2076 2094 7.951347 AAAACTAGATCATCCAAAGCAGAAT 57.049 32.000 0.00 0.00 0.00 2.40
2192 2210 4.251268 GTGAACGAAGCCTACCTTTACAT 58.749 43.478 0.00 0.00 32.78 2.29
2495 2521 8.700051 ACTCATGCTAGATAATTCACAGTAGTT 58.300 33.333 0.00 0.00 0.00 2.24
2524 2550 6.913170 TGTTTCAAAGTTCTAATCATCAGCC 58.087 36.000 0.00 0.00 0.00 4.85
2612 2638 9.630098 GAAAGAATGTTTCTGCTGATTAATGAA 57.370 29.630 0.00 0.00 40.59 2.57
2631 2694 9.950680 TTAATGAACACTTCTCAGTTTTTCATC 57.049 29.630 8.46 0.00 39.89 2.92
2752 2823 4.725790 ATTGGCTTTCAGATGCTTAACC 57.274 40.909 0.00 0.00 0.00 2.85
2795 2866 9.341899 GTTCTATGTCACCACATTTTATTGAAC 57.658 33.333 0.00 0.00 40.66 3.18
2834 2905 5.517322 AATTCTACTGTAGATGGACGACC 57.483 43.478 17.60 0.00 34.22 4.79
2856 2927 2.673775 TTTCTGGATTGGCTGGTTCA 57.326 45.000 0.00 0.00 0.00 3.18
2903 2974 6.102897 AGTAATGTGTCACTCTTTACAGCT 57.897 37.500 14.60 0.00 31.97 4.24
2907 2978 4.119862 TGTGTCACTCTTTACAGCTTCAC 58.880 43.478 4.27 0.00 0.00 3.18
2924 2995 6.148480 CAGCTTCACTGTCTTTACTAGCATTT 59.852 38.462 0.00 0.00 41.86 2.32
2964 3035 2.659063 GGGGGAATTGTTGCAGCCC 61.659 63.158 0.00 0.00 38.08 5.19
3001 3072 5.768980 AGAAGAGGATTCACTTGGATTCA 57.231 39.130 0.00 0.00 0.00 2.57
3009 3080 7.381323 AGGATTCACTTGGATTCATTTTTGAC 58.619 34.615 0.00 0.00 0.00 3.18
3012 3083 6.384258 TCACTTGGATTCATTTTTGACGAA 57.616 33.333 0.00 0.00 0.00 3.85
3026 3097 4.811555 TTGACGAACACCAATTCAAGAG 57.188 40.909 0.00 0.00 0.00 2.85
3051 3122 8.995577 AGGATTTGGATGGATCATTTAATGTTT 58.004 29.630 4.77 0.00 0.00 2.83
3060 3131 9.603921 ATGGATCATTTAATGTTTCATTGTTCC 57.396 29.630 4.77 4.55 0.00 3.62
3093 3164 1.466167 CCAGCAGTTATGTGTCACAGC 59.534 52.381 12.03 8.78 0.00 4.40
3211 3282 5.241403 TCCTGAGGTTCAATGTTGTATGT 57.759 39.130 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 1.261480 ACGAGAGGCAGTGAGTGAAT 58.739 50.000 0.00 0.00 0.00 2.57
128 129 0.102663 GCTAGGGTTGTACGAGAGGC 59.897 60.000 0.00 0.00 0.00 4.70
611 614 9.871238 TTAGCACTTTTTCGATTAGACTTATCT 57.129 29.630 0.38 0.00 39.15 1.98
626 629 9.643693 CTGATGTTGGAAATATTAGCACTTTTT 57.356 29.630 0.00 0.00 25.46 1.94
652 655 1.400494 GATTTGTCATGTGCCCGTACC 59.600 52.381 0.00 0.00 0.00 3.34
653 656 1.062002 CGATTTGTCATGTGCCCGTAC 59.938 52.381 0.00 0.00 0.00 3.67
654 657 1.066787 TCGATTTGTCATGTGCCCGTA 60.067 47.619 0.00 0.00 0.00 4.02
655 658 0.321210 TCGATTTGTCATGTGCCCGT 60.321 50.000 0.00 0.00 0.00 5.28
656 659 0.801872 TTCGATTTGTCATGTGCCCG 59.198 50.000 0.00 0.00 0.00 6.13
657 660 1.539388 TGTTCGATTTGTCATGTGCCC 59.461 47.619 0.00 0.00 0.00 5.36
658 661 2.987413 TGTTCGATTTGTCATGTGCC 57.013 45.000 0.00 0.00 0.00 5.01
659 662 5.827568 AAAATGTTCGATTTGTCATGTGC 57.172 34.783 0.00 0.00 0.00 4.57
660 663 7.392234 TGAAAAATGTTCGATTTGTCATGTG 57.608 32.000 0.00 0.00 32.13 3.21
663 666 7.866898 TGTCATGAAAAATGTTCGATTTGTCAT 59.133 29.630 9.04 9.04 43.18 3.06
664 667 7.199078 TGTCATGAAAAATGTTCGATTTGTCA 58.801 30.769 0.00 5.54 38.96 3.58
665 668 7.621832 TGTCATGAAAAATGTTCGATTTGTC 57.378 32.000 0.00 0.00 0.00 3.18
666 669 7.706179 ACTTGTCATGAAAAATGTTCGATTTGT 59.294 29.630 0.00 0.00 0.00 2.83
667 670 8.064447 ACTTGTCATGAAAAATGTTCGATTTG 57.936 30.769 0.00 0.00 0.00 2.32
668 671 8.647143 AACTTGTCATGAAAAATGTTCGATTT 57.353 26.923 0.00 0.00 0.00 2.17
669 672 7.920151 TGAACTTGTCATGAAAAATGTTCGATT 59.080 29.630 18.67 0.00 36.38 3.34
670 673 7.424803 TGAACTTGTCATGAAAAATGTTCGAT 58.575 30.769 18.67 0.00 36.38 3.59
671 674 6.790282 TGAACTTGTCATGAAAAATGTTCGA 58.210 32.000 18.67 10.19 36.38 3.71
672 675 6.692681 ACTGAACTTGTCATGAAAAATGTTCG 59.307 34.615 18.67 16.23 36.38 3.95
673 676 7.701924 TCACTGAACTTGTCATGAAAAATGTTC 59.298 33.333 17.77 17.77 35.07 3.18
674 677 7.546358 TCACTGAACTTGTCATGAAAAATGTT 58.454 30.769 0.00 0.00 35.07 2.71
675 678 7.099266 TCACTGAACTTGTCATGAAAAATGT 57.901 32.000 0.00 0.00 35.07 2.71
676 679 7.358931 GCATCACTGAACTTGTCATGAAAAATG 60.359 37.037 0.00 0.00 35.07 2.32
677 680 6.643770 GCATCACTGAACTTGTCATGAAAAAT 59.356 34.615 0.00 0.00 35.07 1.82
678 681 5.978919 GCATCACTGAACTTGTCATGAAAAA 59.021 36.000 0.00 0.00 35.07 1.94
679 682 5.067544 TGCATCACTGAACTTGTCATGAAAA 59.932 36.000 0.00 0.00 35.07 2.29
680 683 4.579753 TGCATCACTGAACTTGTCATGAAA 59.420 37.500 0.00 0.00 35.07 2.69
681 684 4.136051 TGCATCACTGAACTTGTCATGAA 58.864 39.130 0.00 0.00 35.07 2.57
682 685 3.742385 TGCATCACTGAACTTGTCATGA 58.258 40.909 0.00 0.00 35.07 3.07
683 686 4.473199 CTTGCATCACTGAACTTGTCATG 58.527 43.478 0.00 0.00 35.07 3.07
684 687 3.504906 CCTTGCATCACTGAACTTGTCAT 59.495 43.478 0.00 0.00 35.07 3.06
685 688 2.880268 CCTTGCATCACTGAACTTGTCA 59.120 45.455 0.00 0.00 34.17 3.58
686 689 3.141398 TCCTTGCATCACTGAACTTGTC 58.859 45.455 0.00 0.00 0.00 3.18
687 690 3.213206 TCCTTGCATCACTGAACTTGT 57.787 42.857 0.00 0.00 0.00 3.16
688 691 3.754850 TCATCCTTGCATCACTGAACTTG 59.245 43.478 0.00 0.00 0.00 3.16
689 692 3.755378 GTCATCCTTGCATCACTGAACTT 59.245 43.478 0.00 0.00 0.00 2.66
690 693 3.244665 TGTCATCCTTGCATCACTGAACT 60.245 43.478 0.00 0.00 0.00 3.01
691 694 3.076621 TGTCATCCTTGCATCACTGAAC 58.923 45.455 0.00 0.00 0.00 3.18
692 695 3.421919 TGTCATCCTTGCATCACTGAA 57.578 42.857 0.00 0.00 0.00 3.02
693 696 3.421919 TTGTCATCCTTGCATCACTGA 57.578 42.857 0.00 0.00 0.00 3.41
694 697 4.713824 AATTGTCATCCTTGCATCACTG 57.286 40.909 0.00 0.00 0.00 3.66
695 698 5.733620 AAAATTGTCATCCTTGCATCACT 57.266 34.783 0.00 0.00 0.00 3.41
696 699 6.624423 ACTAAAATTGTCATCCTTGCATCAC 58.376 36.000 0.00 0.00 0.00 3.06
697 700 6.839124 ACTAAAATTGTCATCCTTGCATCA 57.161 33.333 0.00 0.00 0.00 3.07
698 701 6.532657 CCAACTAAAATTGTCATCCTTGCATC 59.467 38.462 0.00 0.00 0.00 3.91
699 702 6.400568 CCAACTAAAATTGTCATCCTTGCAT 58.599 36.000 0.00 0.00 0.00 3.96
700 703 5.782047 CCAACTAAAATTGTCATCCTTGCA 58.218 37.500 0.00 0.00 0.00 4.08
701 704 4.627035 GCCAACTAAAATTGTCATCCTTGC 59.373 41.667 0.00 0.00 0.00 4.01
702 705 5.782047 TGCCAACTAAAATTGTCATCCTTG 58.218 37.500 0.00 0.00 0.00 3.61
703 706 6.418057 TTGCCAACTAAAATTGTCATCCTT 57.582 33.333 0.00 0.00 0.00 3.36
704 707 6.267471 TCTTTGCCAACTAAAATTGTCATCCT 59.733 34.615 0.00 0.00 0.00 3.24
705 708 6.454795 TCTTTGCCAACTAAAATTGTCATCC 58.545 36.000 0.00 0.00 0.00 3.51
706 709 7.814107 TCATCTTTGCCAACTAAAATTGTCATC 59.186 33.333 0.00 0.00 0.00 2.92
707 710 7.599998 GTCATCTTTGCCAACTAAAATTGTCAT 59.400 33.333 0.00 0.00 0.00 3.06
708 711 6.922957 GTCATCTTTGCCAACTAAAATTGTCA 59.077 34.615 0.00 0.00 0.00 3.58
709 712 6.922957 TGTCATCTTTGCCAACTAAAATTGTC 59.077 34.615 0.00 0.00 0.00 3.18
710 713 6.815089 TGTCATCTTTGCCAACTAAAATTGT 58.185 32.000 0.00 0.00 0.00 2.71
711 714 7.439056 AGTTGTCATCTTTGCCAACTAAAATTG 59.561 33.333 0.97 0.00 32.02 2.32
712 715 7.500141 AGTTGTCATCTTTGCCAACTAAAATT 58.500 30.769 0.97 0.00 32.02 1.82
713 716 7.054491 AGTTGTCATCTTTGCCAACTAAAAT 57.946 32.000 0.97 0.00 32.02 1.82
714 717 6.463995 AGTTGTCATCTTTGCCAACTAAAA 57.536 33.333 0.97 0.00 32.02 1.52
715 718 6.463995 AAGTTGTCATCTTTGCCAACTAAA 57.536 33.333 3.20 0.00 33.25 1.85
716 719 6.463995 AAAGTTGTCATCTTTGCCAACTAA 57.536 33.333 7.89 0.00 34.43 2.24
717 720 6.463995 AAAAGTTGTCATCTTTGCCAACTA 57.536 33.333 9.19 0.00 35.65 2.24
718 721 5.343307 AAAAGTTGTCATCTTTGCCAACT 57.657 34.783 9.19 0.00 35.65 3.16
740 743 6.416455 CGCACTAAAGCATGAAGTTGTAAAAA 59.584 34.615 0.00 0.00 0.00 1.94
741 744 5.912396 CGCACTAAAGCATGAAGTTGTAAAA 59.088 36.000 0.00 0.00 0.00 1.52
742 745 5.448438 CGCACTAAAGCATGAAGTTGTAAA 58.552 37.500 0.00 0.00 0.00 2.01
743 746 4.612712 GCGCACTAAAGCATGAAGTTGTAA 60.613 41.667 0.30 0.00 0.00 2.41
744 747 3.120338 GCGCACTAAAGCATGAAGTTGTA 60.120 43.478 0.30 0.00 0.00 2.41
745 748 2.350772 GCGCACTAAAGCATGAAGTTGT 60.351 45.455 0.30 0.00 0.00 3.32
746 749 2.245096 GCGCACTAAAGCATGAAGTTG 58.755 47.619 0.30 0.00 0.00 3.16
747 750 1.135972 CGCGCACTAAAGCATGAAGTT 60.136 47.619 8.75 0.00 0.00 2.66
748 751 0.443869 CGCGCACTAAAGCATGAAGT 59.556 50.000 8.75 0.00 0.00 3.01
753 756 2.452813 CCGACGCGCACTAAAGCAT 61.453 57.895 5.73 0.00 0.00 3.79
822 826 2.367377 TCATGGGCCTAGGCTGCT 60.367 61.111 32.18 14.49 41.60 4.24
873 877 1.125093 TTGCCCCAGAAAGAGGTCGA 61.125 55.000 0.00 0.00 0.00 4.20
902 906 4.733542 AATGGTCGGCCGGGTTGG 62.734 66.667 27.83 0.00 42.50 3.77
908 912 2.582498 GACGAGAATGGTCGGCCG 60.582 66.667 22.12 22.12 42.55 6.13
915 919 2.444256 GGGGAGGGGACGAGAATGG 61.444 68.421 0.00 0.00 0.00 3.16
957 969 2.478890 CGGAGCGGTGGATCTACGT 61.479 63.158 2.84 0.00 32.30 3.57
988 1006 4.471726 GCCCATCGTCGTCGTCGT 62.472 66.667 11.41 0.00 38.33 4.34
1033 1051 1.006805 GGATGAGGATGTCCGCGAG 60.007 63.158 8.23 0.00 42.08 5.03
1200 1218 4.111053 GGGAGGGCGGGGAAGAAC 62.111 72.222 0.00 0.00 0.00 3.01
1455 1473 1.911702 GCTGGAGGTAGGGGTTGTCC 61.912 65.000 0.00 0.00 0.00 4.02
1564 1582 1.300465 CCATCCAGATGACGGCGAG 60.300 63.158 16.62 0.00 41.20 5.03
1613 1631 1.110442 CCGAGATCCAGAGCAGAAGT 58.890 55.000 0.00 0.00 0.00 3.01
1774 1792 0.171231 GAGAACTCCATTTTGCGGGC 59.829 55.000 0.00 0.00 0.00 6.13
1869 1887 1.228154 AACGGTTGTCCTGCCTTCC 60.228 57.895 0.00 0.00 0.00 3.46
1893 1911 1.555992 TCCGCCCTAAAAAGATCCGAA 59.444 47.619 0.00 0.00 0.00 4.30
1896 1914 5.826208 TCTTTTATCCGCCCTAAAAAGATCC 59.174 40.000 5.28 0.00 40.92 3.36
1980 1998 0.181350 ATTCCTCGGGCAAGGTGATC 59.819 55.000 5.22 0.00 37.69 2.92
1992 2010 2.797278 CCGGTCTCCCCATTCCTCG 61.797 68.421 0.00 0.00 0.00 4.63
2049 2067 8.442632 TCTGCTTTGGATGATCTAGTTTTATG 57.557 34.615 0.00 0.00 0.00 1.90
2055 2073 7.330900 CAAATTCTGCTTTGGATGATCTAGT 57.669 36.000 0.00 0.00 33.42 2.57
2076 2094 1.704628 TGCTCAACAGGATCTCCCAAA 59.295 47.619 0.00 0.00 37.41 3.28
2311 2337 8.118976 TCTAGTATGGCATAACGCTAAACTAT 57.881 34.615 9.14 0.00 41.91 2.12
2354 2380 8.783660 ATTCTCCAGAAGACATAACCATACTA 57.216 34.615 0.00 0.00 37.48 1.82
2435 2461 8.114331 TCATTTTGTTGTGATTCTAGAGCAAT 57.886 30.769 0.00 0.00 0.00 3.56
2449 2475 8.605746 CATGAGTTGTTTTCATCATTTTGTTGT 58.394 29.630 0.00 0.00 33.14 3.32
2495 2521 9.958180 TGATGATTAGAACTTTGAAACATCCTA 57.042 29.630 0.00 0.00 33.22 2.94
2502 2528 5.391950 GCGGCTGATGATTAGAACTTTGAAA 60.392 40.000 0.00 0.00 0.00 2.69
2524 2550 4.032355 AAACAACACGTTTTAGATGTGCG 58.968 39.130 0.00 0.00 45.79 5.34
2612 2638 6.206243 CCATGAGATGAAAAACTGAGAAGTGT 59.794 38.462 0.00 0.00 0.00 3.55
2752 2823 3.408634 AGAACCCTTAAACCATGTCACG 58.591 45.455 0.00 0.00 0.00 4.35
2834 2905 1.755179 ACCAGCCAATCCAGAAATCG 58.245 50.000 0.00 0.00 0.00 3.34
2856 2927 1.928868 CACCCTTTTCCAGCTCCAAT 58.071 50.000 0.00 0.00 0.00 3.16
2903 2974 8.220755 ACAAAAATGCTAGTAAAGACAGTGAA 57.779 30.769 0.00 0.00 0.00 3.18
2907 2978 8.116753 CCGATACAAAAATGCTAGTAAAGACAG 58.883 37.037 0.00 0.00 0.00 3.51
2947 3018 1.610379 AGGGCTGCAACAATTCCCC 60.610 57.895 0.50 0.00 37.70 4.81
2964 3035 3.135530 CCTCTTCTATTCCCCACTTCCAG 59.864 52.174 0.00 0.00 0.00 3.86
3001 3072 6.568869 TCTTGAATTGGTGTTCGTCAAAAAT 58.431 32.000 0.00 0.00 0.00 1.82
3009 3080 5.156355 CAAATCCTCTTGAATTGGTGTTCG 58.844 41.667 0.00 0.00 31.42 3.95
3026 3097 9.264719 GAAACATTAAATGATCCATCCAAATCC 57.735 33.333 0.00 0.00 0.00 3.01
3060 3131 1.476891 ACTGCTGGTACGACTGTATGG 59.523 52.381 0.00 0.00 32.11 2.74
3093 3164 2.346597 GGGCTCGATCAGACCCTAG 58.653 63.158 5.91 0.00 46.65 3.02


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

AutoCloner maintained by Alex Coulton.