Multiple sequence alignment - TraesCS5A01G122000

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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 TraesCS5A01G122000 chr5A 100.000 4360 0 0 1 4360 264748708 264753067 0.000000e+00 8052.0
1 TraesCS5A01G122000 chr5A 97.389 3715 82 11 657 4360 283460105 283463815 0.000000e+00 6309.0
2 TraesCS5A01G122000 chr5A 96.983 3679 102 9 687 4360 337714274 337710600 0.000000e+00 6170.0
3 TraesCS5A01G122000 chr4B 95.302 1639 68 7 2624 4256 136783240 136784875 0.000000e+00 2591.0
4 TraesCS5A01G122000 chr4B 92.948 1659 83 19 691 2317 136781091 136782747 0.000000e+00 2385.0
5 TraesCS5A01G122000 chr4B 94.454 613 29 4 3646 4256 187391198 187391807 0.000000e+00 939.0
6 TraesCS5A01G122000 chr4B 97.908 239 5 0 2391 2629 136782964 136783202 8.720000e-112 414.0
7 TraesCS5A01G122000 chr4B 98.413 63 1 0 4293 4355 136785373 136785435 1.280000e-20 111.0
8 TraesCS5A01G122000 chr4B 95.238 63 3 0 4293 4355 187392305 187392367 2.770000e-17 100.0
9 TraesCS5A01G122000 chr3B 95.293 1636 66 6 2627 4256 230194481 230192851 0.000000e+00 2584.0
10 TraesCS5A01G122000 chr3B 94.695 1640 78 7 2624 4256 266165347 266166984 0.000000e+00 2538.0
11 TraesCS5A01G122000 chr3B 93.716 1655 67 11 700 2320 230196625 230194974 0.000000e+00 2446.0
12 TraesCS5A01G122000 chr3B 92.797 1652 84 9 694 2317 266163210 266164854 0.000000e+00 2359.0
13 TraesCS5A01G122000 chr3B 90.936 1688 113 16 2627 4297 278848645 278850309 0.000000e+00 2233.0
14 TraesCS5A01G122000 chr3B 88.978 1497 127 27 839 2317 278846676 278848152 0.000000e+00 1816.0
15 TraesCS5A01G122000 chr3B 98.326 239 4 0 2391 2629 230194760 230194522 1.880000e-113 420.0
16 TraesCS5A01G122000 chr3B 96.653 239 8 0 2391 2629 266165071 266165309 8.790000e-107 398.0
17 TraesCS5A01G122000 chr3B 93.333 240 12 3 2391 2629 278848368 278848604 6.940000e-93 351.0
18 TraesCS5A01G122000 chr3B 88.679 159 14 3 681 835 278846476 278846634 1.600000e-44 191.0
19 TraesCS5A01G122000 chr3B 98.413 63 1 0 4293 4355 266167475 266167537 1.280000e-20 111.0
20 TraesCS5A01G122000 chr3B 96.825 63 2 0 4293 4355 230192352 230192290 5.960000e-19 106.0
21 TraesCS5A01G122000 chr3B 93.651 63 4 0 4293 4355 278850784 278850846 1.290000e-15 95.3
22 TraesCS5A01G122000 chr3D 92.630 1574 92 15 2627 4187 339595132 339593570 0.000000e+00 2242.0
23 TraesCS5A01G122000 chr3D 88.452 1195 100 24 667 1829 339597919 339596731 0.000000e+00 1408.0
24 TraesCS5A01G122000 chr3D 94.746 571 29 1 1 570 360726952 360726382 0.000000e+00 887.0
25 TraesCS5A01G122000 chr3D 94.138 580 29 4 1 579 525398364 525398939 0.000000e+00 878.0
26 TraesCS5A01G122000 chr3D 94.583 240 10 2 2391 2629 339595410 339595173 6.890000e-98 368.0
27 TraesCS5A01G122000 chr3D 96.825 63 2 0 4293 4355 339593047 339592985 5.960000e-19 106.0
28 TraesCS5A01G122000 chr5B 90.349 1689 113 17 2627 4297 457602983 457604639 0.000000e+00 2170.0
29 TraesCS5A01G122000 chr5B 88.946 1158 103 19 838 1978 457589662 457590811 0.000000e+00 1406.0
30 TraesCS5A01G122000 chr5B 94.191 241 10 3 2391 2629 457602706 457602944 8.910000e-97 364.0
31 TraesCS5A01G122000 chr2D 92.940 1473 88 9 2627 4089 300441990 300440524 0.000000e+00 2130.0
32 TraesCS5A01G122000 chr2D 89.204 1695 138 25 2624 4297 430787279 430788949 0.000000e+00 2074.0
33 TraesCS5A01G122000 chr2D 89.200 1500 131 24 838 2317 430785298 430786786 0.000000e+00 1844.0
34 TraesCS5A01G122000 chr2D 90.983 1353 107 13 974 2320 300443823 300442480 0.000000e+00 1808.0
35 TraesCS5A01G122000 chr2D 94.746 571 29 1 1 570 301940334 301940904 0.000000e+00 887.0
36 TraesCS5A01G122000 chr2D 93.750 240 11 3 2391 2629 300442267 300442031 1.490000e-94 357.0
37 TraesCS5A01G122000 chr2D 96.825 63 2 0 4293 4355 300425192 300425130 5.960000e-19 106.0
38 TraesCS5A01G122000 chr2D 92.857 56 3 1 897 952 300444742 300444688 3.610000e-11 80.5
39 TraesCS5A01G122000 chr2D 94.118 51 1 2 903 953 300445085 300445037 4.680000e-10 76.8
40 TraesCS5A01G122000 chr2D 90.566 53 3 2 897 949 430785293 430785343 7.820000e-08 69.4
41 TraesCS5A01G122000 chr7B 90.502 1474 100 14 2627 4082 599500782 599502233 0.000000e+00 1910.0
42 TraesCS5A01G122000 chr7B 88.331 1474 146 18 864 2317 599498822 599500289 0.000000e+00 1746.0
43 TraesCS5A01G122000 chr6D 94.746 571 29 1 1 570 99850621 99850051 0.000000e+00 887.0
44 TraesCS5A01G122000 chr6D 94.746 571 29 1 1 570 284747783 284748353 0.000000e+00 887.0
45 TraesCS5A01G122000 chr4D 94.746 571 28 2 1 570 371852857 371853426 0.000000e+00 887.0
46 TraesCS5A01G122000 chr4D 89.610 154 13 3 682 835 270368795 270368945 4.450000e-45 193.0
47 TraesCS5A01G122000 chr1A 94.755 572 27 3 1 570 127441425 127441995 0.000000e+00 887.0
48 TraesCS5A01G122000 chr5D 94.571 571 30 1 1 570 336581241 336581811 0.000000e+00 881.0
49 TraesCS5A01G122000 chr4A 94.148 581 31 2 1 578 82216780 82216200 0.000000e+00 881.0
50 TraesCS5A01G122000 chr7D 93.571 140 5 3 657 793 30996531 30996669 5.720000e-49 206.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G122000 chr5A 264748708 264753067 4359 False 8052.000000 8052 100.000000 1 4360 1 chr5A.!!$F1 4359
1 TraesCS5A01G122000 chr5A 283460105 283463815 3710 False 6309.000000 6309 97.389000 657 4360 1 chr5A.!!$F2 3703
2 TraesCS5A01G122000 chr5A 337710600 337714274 3674 True 6170.000000 6170 96.983000 687 4360 1 chr5A.!!$R1 3673
3 TraesCS5A01G122000 chr4B 136781091 136785435 4344 False 1375.250000 2591 96.142750 691 4355 4 chr4B.!!$F1 3664
4 TraesCS5A01G122000 chr4B 187391198 187392367 1169 False 519.500000 939 94.846000 3646 4355 2 chr4B.!!$F2 709
5 TraesCS5A01G122000 chr3B 230192290 230196625 4335 True 1389.000000 2584 96.040000 700 4355 4 chr3B.!!$R1 3655
6 TraesCS5A01G122000 chr3B 266163210 266167537 4327 False 1351.500000 2538 95.639500 694 4355 4 chr3B.!!$F1 3661
7 TraesCS5A01G122000 chr3B 278846476 278850846 4370 False 937.260000 2233 91.115400 681 4355 5 chr3B.!!$F2 3674
8 TraesCS5A01G122000 chr3D 339592985 339597919 4934 True 1031.000000 2242 93.122500 667 4355 4 chr3D.!!$R2 3688
9 TraesCS5A01G122000 chr3D 360726382 360726952 570 True 887.000000 887 94.746000 1 570 1 chr3D.!!$R1 569
10 TraesCS5A01G122000 chr3D 525398364 525398939 575 False 878.000000 878 94.138000 1 579 1 chr3D.!!$F1 578
11 TraesCS5A01G122000 chr5B 457589662 457590811 1149 False 1406.000000 1406 88.946000 838 1978 1 chr5B.!!$F1 1140
12 TraesCS5A01G122000 chr5B 457602706 457604639 1933 False 1267.000000 2170 92.270000 2391 4297 2 chr5B.!!$F2 1906
13 TraesCS5A01G122000 chr2D 430785293 430788949 3656 False 1329.133333 2074 89.656667 838 4297 3 chr2D.!!$F2 3459
14 TraesCS5A01G122000 chr2D 300440524 300445085 4561 True 890.460000 2130 92.929600 897 4089 5 chr2D.!!$R2 3192
15 TraesCS5A01G122000 chr2D 301940334 301940904 570 False 887.000000 887 94.746000 1 570 1 chr2D.!!$F1 569
16 TraesCS5A01G122000 chr7B 599498822 599502233 3411 False 1828.000000 1910 89.416500 864 4082 2 chr7B.!!$F1 3218
17 TraesCS5A01G122000 chr6D 99850051 99850621 570 True 887.000000 887 94.746000 1 570 1 chr6D.!!$R1 569
18 TraesCS5A01G122000 chr6D 284747783 284748353 570 False 887.000000 887 94.746000 1 570 1 chr6D.!!$F1 569
19 TraesCS5A01G122000 chr4D 371852857 371853426 569 False 887.000000 887 94.746000 1 570 1 chr4D.!!$F2 569
20 TraesCS5A01G122000 chr1A 127441425 127441995 570 False 887.000000 887 94.755000 1 570 1 chr1A.!!$F1 569
21 TraesCS5A01G122000 chr5D 336581241 336581811 570 False 881.000000 881 94.571000 1 570 1 chr5D.!!$F1 569
22 TraesCS5A01G122000 chr4A 82216200 82216780 580 True 881.000000 881 94.148000 1 578 1 chr4A.!!$R1 577

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
71 72 0.108804 ACAATCTACACGCCGGACTG 60.109 55.000 5.05 0.3 0.00 3.51 F
660 664 0.325296 ACCCGCCTGAGGTTCATCTA 60.325 55.000 0.00 0.0 32.05 1.98 F
1169 2015 1.003928 GCCTTTTTCCGTCCTTCCCTA 59.996 52.381 0.00 0.0 0.00 3.53 F
1542 2901 1.066143 GGTTGGTGGTCGAGACATCAT 60.066 52.381 4.04 0.0 0.00 2.45 F
2977 4684 1.838112 AACATGGTGGATGTCGCAAT 58.162 45.000 0.00 0.0 45.12 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 2873 0.959867 CGACCACCAACCATGCATGA 60.960 55.000 28.31 0.0 0.00 3.07 R
1542 2901 1.903877 GCCACCTGCTGAAGCTCCTA 61.904 60.000 3.61 0.0 42.66 2.94 R
2657 4360 4.730042 CGATGGTTTCGTTTTGATGCTATG 59.270 41.667 0.00 0.0 43.01 2.23 R
3085 4795 8.470657 AAGCTATAGATAGATGATAATGCGGA 57.529 34.615 3.21 0.0 32.05 5.54 R
4089 5891 9.128107 CATGCTTAGTTGTGTTTTGTAATTAGG 57.872 33.333 0.00 0.0 0.00 2.69 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
36 37 1.479730 GTATTCGGAGAAGGAACCCGT 59.520 52.381 0.00 0.00 45.90 5.28
71 72 0.108804 ACAATCTACACGCCGGACTG 60.109 55.000 5.05 0.30 0.00 3.51
76 77 3.405592 TACACGCCGGACTGATCGC 62.406 63.158 5.05 0.00 0.00 4.58
120 121 1.007963 ACCGAGGGAGTCCTGGATTAA 59.992 52.381 18.62 0.00 45.05 1.40
171 172 1.117150 GGCCGGACTGTTGGACTATA 58.883 55.000 5.05 0.00 0.00 1.31
262 263 6.393171 TGGCAATTCAGATATGTAGATCTCG 58.607 40.000 0.00 0.00 33.75 4.04
399 402 5.045505 AGCCTCTACGATCTCATGGTAGATA 60.046 44.000 8.34 0.00 45.40 1.98
526 529 0.384309 TACCATCAGCCTTAGACGCG 59.616 55.000 3.53 3.53 0.00 6.01
585 589 2.803203 CGATAGGGAGGTCGTTGGA 58.197 57.895 0.00 0.00 33.42 3.53
586 590 1.108776 CGATAGGGAGGTCGTTGGAA 58.891 55.000 0.00 0.00 33.42 3.53
587 591 1.687123 CGATAGGGAGGTCGTTGGAAT 59.313 52.381 0.00 0.00 33.42 3.01
588 592 2.288273 CGATAGGGAGGTCGTTGGAATC 60.288 54.545 0.00 0.00 33.42 2.52
589 593 1.492764 TAGGGAGGTCGTTGGAATCC 58.507 55.000 0.00 0.00 32.15 3.01
590 594 1.223763 GGGAGGTCGTTGGAATCCC 59.776 63.158 0.00 0.00 41.04 3.85
591 595 1.559065 GGGAGGTCGTTGGAATCCCA 61.559 60.000 3.68 0.00 44.50 4.37
600 604 1.651737 TTGGAATCCCAAGTCCGAGA 58.348 50.000 0.00 0.00 46.94 4.04
601 605 1.195115 TGGAATCCCAAGTCCGAGAG 58.805 55.000 0.00 0.00 42.74 3.20
602 606 1.273041 TGGAATCCCAAGTCCGAGAGA 60.273 52.381 0.00 0.00 42.74 3.10
603 607 1.831736 GGAATCCCAAGTCCGAGAGAA 59.168 52.381 0.00 0.00 28.45 2.87
604 608 2.418884 GGAATCCCAAGTCCGAGAGAAC 60.419 54.545 0.00 0.00 28.45 3.01
605 609 2.239681 ATCCCAAGTCCGAGAGAACT 57.760 50.000 0.00 0.00 0.00 3.01
606 610 1.257743 TCCCAAGTCCGAGAGAACTG 58.742 55.000 0.00 0.00 0.00 3.16
607 611 0.390472 CCCAAGTCCGAGAGAACTGC 60.390 60.000 0.00 0.00 0.00 4.40
608 612 0.605589 CCAAGTCCGAGAGAACTGCT 59.394 55.000 0.00 0.00 0.00 4.24
609 613 1.671261 CCAAGTCCGAGAGAACTGCTG 60.671 57.143 0.00 0.00 0.00 4.41
610 614 1.270826 CAAGTCCGAGAGAACTGCTGA 59.729 52.381 0.00 0.00 0.00 4.26
611 615 1.173043 AGTCCGAGAGAACTGCTGAG 58.827 55.000 0.00 0.00 0.00 3.35
612 616 0.885196 GTCCGAGAGAACTGCTGAGT 59.115 55.000 0.00 0.00 0.00 3.41
613 617 0.884514 TCCGAGAGAACTGCTGAGTG 59.115 55.000 0.00 0.00 30.61 3.51
614 618 0.884514 CCGAGAGAACTGCTGAGTGA 59.115 55.000 0.00 0.00 30.61 3.41
615 619 1.402194 CCGAGAGAACTGCTGAGTGAC 60.402 57.143 0.00 0.00 30.61 3.67
616 620 1.402194 CGAGAGAACTGCTGAGTGACC 60.402 57.143 0.00 0.00 30.61 4.02
617 621 1.615883 GAGAGAACTGCTGAGTGACCA 59.384 52.381 0.00 0.00 30.61 4.02
618 622 2.036475 GAGAGAACTGCTGAGTGACCAA 59.964 50.000 0.00 0.00 30.61 3.67
619 623 2.036992 AGAGAACTGCTGAGTGACCAAG 59.963 50.000 0.00 0.00 30.61 3.61
620 624 1.765314 AGAACTGCTGAGTGACCAAGT 59.235 47.619 0.00 0.00 30.61 3.16
621 625 2.171448 AGAACTGCTGAGTGACCAAGTT 59.829 45.455 0.00 0.00 30.61 2.66
622 626 2.717639 ACTGCTGAGTGACCAAGTTT 57.282 45.000 0.00 0.00 0.00 2.66
623 627 2.292267 ACTGCTGAGTGACCAAGTTTG 58.708 47.619 0.00 0.00 0.00 2.93
624 628 2.092968 ACTGCTGAGTGACCAAGTTTGA 60.093 45.455 0.00 0.00 0.00 2.69
625 629 2.547211 CTGCTGAGTGACCAAGTTTGAG 59.453 50.000 0.00 0.00 0.00 3.02
626 630 2.092968 TGCTGAGTGACCAAGTTTGAGT 60.093 45.455 0.00 0.00 0.00 3.41
627 631 3.133901 TGCTGAGTGACCAAGTTTGAGTA 59.866 43.478 0.00 0.00 0.00 2.59
628 632 3.743396 GCTGAGTGACCAAGTTTGAGTAG 59.257 47.826 0.00 0.00 0.00 2.57
629 633 3.728845 TGAGTGACCAAGTTTGAGTAGC 58.271 45.455 0.00 0.00 0.00 3.58
630 634 3.388024 TGAGTGACCAAGTTTGAGTAGCT 59.612 43.478 0.00 0.00 0.00 3.32
631 635 3.991121 GAGTGACCAAGTTTGAGTAGCTC 59.009 47.826 0.00 0.00 0.00 4.09
632 636 3.388024 AGTGACCAAGTTTGAGTAGCTCA 59.612 43.478 0.00 0.00 38.87 4.26
633 637 4.127171 GTGACCAAGTTTGAGTAGCTCAA 58.873 43.478 7.41 7.41 46.93 3.02
642 646 3.876274 TGAGTAGCTCAACCATCTGAC 57.124 47.619 0.00 0.00 37.57 3.51
643 647 2.497675 TGAGTAGCTCAACCATCTGACC 59.502 50.000 0.00 0.00 37.57 4.02
644 648 1.834263 AGTAGCTCAACCATCTGACCC 59.166 52.381 0.00 0.00 0.00 4.46
645 649 0.824109 TAGCTCAACCATCTGACCCG 59.176 55.000 0.00 0.00 0.00 5.28
646 650 2.109126 GCTCAACCATCTGACCCGC 61.109 63.158 0.00 0.00 0.00 6.13
647 651 1.450312 CTCAACCATCTGACCCGCC 60.450 63.158 0.00 0.00 0.00 6.13
648 652 1.903877 CTCAACCATCTGACCCGCCT 61.904 60.000 0.00 0.00 0.00 5.52
649 653 1.746615 CAACCATCTGACCCGCCTG 60.747 63.158 0.00 0.00 0.00 4.85
650 654 1.918293 AACCATCTGACCCGCCTGA 60.918 57.895 0.00 0.00 0.00 3.86
651 655 1.903877 AACCATCTGACCCGCCTGAG 61.904 60.000 0.00 0.00 0.00 3.35
652 656 2.503061 CATCTGACCCGCCTGAGG 59.497 66.667 0.00 0.00 0.00 3.86
653 657 2.039624 ATCTGACCCGCCTGAGGT 59.960 61.111 0.00 0.00 41.50 3.85
654 658 1.613630 ATCTGACCCGCCTGAGGTT 60.614 57.895 0.00 0.00 37.88 3.50
655 659 1.617947 ATCTGACCCGCCTGAGGTTC 61.618 60.000 0.00 0.00 37.88 3.62
656 660 2.525629 TGACCCGCCTGAGGTTCA 60.526 61.111 0.00 0.00 37.88 3.18
657 661 1.903877 CTGACCCGCCTGAGGTTCAT 61.904 60.000 0.00 0.00 37.88 2.57
658 662 1.153349 GACCCGCCTGAGGTTCATC 60.153 63.158 0.00 0.00 37.88 2.92
659 663 1.613630 ACCCGCCTGAGGTTCATCT 60.614 57.895 0.00 0.00 32.05 2.90
660 664 0.325296 ACCCGCCTGAGGTTCATCTA 60.325 55.000 0.00 0.00 32.05 1.98
661 665 1.051812 CCCGCCTGAGGTTCATCTAT 58.948 55.000 0.00 0.00 0.00 1.98
662 666 2.248248 CCCGCCTGAGGTTCATCTATA 58.752 52.381 0.00 0.00 0.00 1.31
671 675 8.846211 GCCTGAGGTTCATCTATATCTATCTAC 58.154 40.741 0.00 0.00 0.00 2.59
846 897 5.669164 AAAGCTCCAAAACCTAAAACACA 57.331 34.783 0.00 0.00 0.00 3.72
1169 2015 1.003928 GCCTTTTTCCGTCCTTCCCTA 59.996 52.381 0.00 0.00 0.00 3.53
1309 2155 2.637872 TCTTCCTCACCTCGAATTGGTT 59.362 45.455 0.00 0.00 35.28 3.67
1312 2158 1.522668 CTCACCTCGAATTGGTTGCA 58.477 50.000 0.00 0.00 35.28 4.08
1514 2873 3.141488 CCTACCTCGAGCGGCACT 61.141 66.667 6.99 0.00 0.00 4.40
1542 2901 1.066143 GGTTGGTGGTCGAGACATCAT 60.066 52.381 4.04 0.00 0.00 2.45
1584 2943 5.123979 GCGTTGATCCAAAATTACTCCTTCT 59.876 40.000 0.00 0.00 0.00 2.85
1713 3072 2.562298 CCAAATTTGCTGAACCAGGCTA 59.438 45.455 12.92 0.00 31.21 3.93
2594 4210 3.935993 GCCTTAGGCTGTCTCACAA 57.064 52.632 17.16 0.00 46.69 3.33
2883 4590 4.511454 TCTTTTGCGTCATGGTATATCTGC 59.489 41.667 0.00 0.00 0.00 4.26
2977 4684 1.838112 AACATGGTGGATGTCGCAAT 58.162 45.000 0.00 0.00 45.12 3.56
3738 5480 2.221749 GTGCATGTCCATACATAGTGCG 59.778 50.000 0.00 0.00 44.70 5.34
4075 5877 8.217778 GTGATGTTTCAAAACTGAAAAACGAAA 58.782 29.630 7.12 0.00 39.20 3.46
4192 5994 7.759433 CCCGTATGCACATTTCTTTCTATTTTT 59.241 33.333 0.00 0.00 0.00 1.94
4236 6038 3.751175 TGAAGTTTAATGCAACCCTCGAG 59.249 43.478 5.13 5.13 0.00 4.04
4355 6664 6.655078 ATTTCTCCAACTATGTTTTGTGCT 57.345 33.333 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.603456 TTGTCTTCGGCATTGCAAGA 58.397 45.000 11.39 8.99 0.00 3.02
71 72 0.749454 ACCAGGCTTCAATGGCGATC 60.749 55.000 0.00 0.00 40.45 3.69
76 77 1.180029 CCTGAACCAGGCTTCAATGG 58.820 55.000 0.00 0.00 45.13 3.16
216 217 1.454847 TTGCCTTCCACGCAAAGGT 60.455 52.632 11.40 0.00 44.34 3.50
262 263 1.617357 ACAGAGTCGGTTACAAGGGAC 59.383 52.381 0.00 0.00 0.00 4.46
340 343 6.830912 AGCTAGCCTGTGATTATGATTGTTA 58.169 36.000 12.13 0.00 0.00 2.41
355 358 3.493524 GCTAAACCCTAGAAGCTAGCCTG 60.494 52.174 12.13 0.00 32.18 4.85
437 440 6.556644 ATGGAGGTAATACCCTACTTCCTA 57.443 41.667 13.63 3.86 44.50 2.94
570 574 1.492764 GGATTCCAACGACCTCCCTA 58.507 55.000 0.00 0.00 0.00 3.53
582 586 1.195115 CTCTCGGACTTGGGATTCCA 58.805 55.000 4.80 0.00 42.25 3.53
583 587 1.486211 TCTCTCGGACTTGGGATTCC 58.514 55.000 0.00 0.00 0.00 3.01
584 588 2.498078 AGTTCTCTCGGACTTGGGATTC 59.502 50.000 0.00 0.00 0.00 2.52
585 589 2.234908 CAGTTCTCTCGGACTTGGGATT 59.765 50.000 0.00 0.00 0.00 3.01
586 590 1.827969 CAGTTCTCTCGGACTTGGGAT 59.172 52.381 0.00 0.00 0.00 3.85
587 591 1.257743 CAGTTCTCTCGGACTTGGGA 58.742 55.000 0.00 0.00 0.00 4.37
588 592 0.390472 GCAGTTCTCTCGGACTTGGG 60.390 60.000 0.00 0.00 0.00 4.12
589 593 0.605589 AGCAGTTCTCTCGGACTTGG 59.394 55.000 0.00 0.00 0.00 3.61
590 594 1.270826 TCAGCAGTTCTCTCGGACTTG 59.729 52.381 0.00 0.00 0.00 3.16
591 595 1.543802 CTCAGCAGTTCTCTCGGACTT 59.456 52.381 0.00 0.00 0.00 3.01
592 596 1.173043 CTCAGCAGTTCTCTCGGACT 58.827 55.000 0.00 0.00 0.00 3.85
593 597 0.885196 ACTCAGCAGTTCTCTCGGAC 59.115 55.000 0.00 0.00 0.00 4.79
594 598 0.884514 CACTCAGCAGTTCTCTCGGA 59.115 55.000 0.00 0.00 0.00 4.55
595 599 0.884514 TCACTCAGCAGTTCTCTCGG 59.115 55.000 0.00 0.00 0.00 4.63
596 600 1.402194 GGTCACTCAGCAGTTCTCTCG 60.402 57.143 0.00 0.00 0.00 4.04
597 601 1.615883 TGGTCACTCAGCAGTTCTCTC 59.384 52.381 0.00 0.00 0.00 3.20
598 602 1.709578 TGGTCACTCAGCAGTTCTCT 58.290 50.000 0.00 0.00 0.00 3.10
599 603 2.224161 ACTTGGTCACTCAGCAGTTCTC 60.224 50.000 0.00 0.00 32.85 2.87
600 604 1.765314 ACTTGGTCACTCAGCAGTTCT 59.235 47.619 0.00 0.00 32.85 3.01
601 605 2.246719 ACTTGGTCACTCAGCAGTTC 57.753 50.000 0.00 0.00 32.85 3.01
602 606 2.684881 CAAACTTGGTCACTCAGCAGTT 59.315 45.455 0.00 0.00 32.85 3.16
603 607 2.092968 TCAAACTTGGTCACTCAGCAGT 60.093 45.455 0.00 0.00 32.85 4.40
604 608 2.547211 CTCAAACTTGGTCACTCAGCAG 59.453 50.000 0.00 0.00 32.85 4.24
605 609 2.092968 ACTCAAACTTGGTCACTCAGCA 60.093 45.455 0.00 0.00 0.00 4.41
606 610 2.565841 ACTCAAACTTGGTCACTCAGC 58.434 47.619 0.00 0.00 0.00 4.26
607 611 3.743396 GCTACTCAAACTTGGTCACTCAG 59.257 47.826 0.00 0.00 0.00 3.35
608 612 3.388024 AGCTACTCAAACTTGGTCACTCA 59.612 43.478 0.00 0.00 0.00 3.41
609 613 3.991121 GAGCTACTCAAACTTGGTCACTC 59.009 47.826 0.00 0.00 0.00 3.51
610 614 3.388024 TGAGCTACTCAAACTTGGTCACT 59.612 43.478 0.00 0.00 37.57 3.41
611 615 3.728845 TGAGCTACTCAAACTTGGTCAC 58.271 45.455 0.00 0.00 37.57 3.67
612 616 4.415881 TTGAGCTACTCAAACTTGGTCA 57.584 40.909 7.54 0.00 45.84 4.02
621 625 3.055819 GGTCAGATGGTTGAGCTACTCAA 60.056 47.826 5.94 5.94 46.50 3.02
622 626 2.497675 GGTCAGATGGTTGAGCTACTCA 59.502 50.000 0.00 0.00 41.23 3.41
623 627 2.159028 GGGTCAGATGGTTGAGCTACTC 60.159 54.545 5.36 0.00 43.33 2.59
624 628 1.834263 GGGTCAGATGGTTGAGCTACT 59.166 52.381 5.36 0.00 43.33 2.57
625 629 1.471676 CGGGTCAGATGGTTGAGCTAC 60.472 57.143 5.36 0.00 43.33 3.58
626 630 0.824109 CGGGTCAGATGGTTGAGCTA 59.176 55.000 5.36 0.00 43.33 3.32
627 631 1.599047 CGGGTCAGATGGTTGAGCT 59.401 57.895 5.36 0.00 43.33 4.09
628 632 2.109126 GCGGGTCAGATGGTTGAGC 61.109 63.158 0.00 0.00 43.13 4.26
629 633 1.450312 GGCGGGTCAGATGGTTGAG 60.450 63.158 0.00 0.00 0.00 3.02
630 634 1.918293 AGGCGGGTCAGATGGTTGA 60.918 57.895 0.00 0.00 0.00 3.18
631 635 1.746615 CAGGCGGGTCAGATGGTTG 60.747 63.158 0.00 0.00 0.00 3.77
632 636 1.903877 CTCAGGCGGGTCAGATGGTT 61.904 60.000 0.00 0.00 0.00 3.67
633 637 2.284625 TCAGGCGGGTCAGATGGT 60.285 61.111 0.00 0.00 0.00 3.55
634 638 2.503061 CTCAGGCGGGTCAGATGG 59.497 66.667 0.00 0.00 0.00 3.51
635 639 1.903877 AACCTCAGGCGGGTCAGATG 61.904 60.000 0.00 0.00 35.83 2.90
636 640 1.613630 AACCTCAGGCGGGTCAGAT 60.614 57.895 0.00 0.00 35.83 2.90
637 641 2.203788 AACCTCAGGCGGGTCAGA 60.204 61.111 0.00 0.00 35.83 3.27
638 642 2.266055 GAACCTCAGGCGGGTCAG 59.734 66.667 0.00 0.00 40.60 3.51
640 644 1.153349 GATGAACCTCAGGCGGGTC 60.153 63.158 0.00 0.00 41.30 4.46
641 645 0.325296 TAGATGAACCTCAGGCGGGT 60.325 55.000 0.00 0.00 38.94 5.28
642 646 1.051812 ATAGATGAACCTCAGGCGGG 58.948 55.000 0.00 0.00 0.00 6.13
643 647 3.766591 AGATATAGATGAACCTCAGGCGG 59.233 47.826 0.00 0.00 0.00 6.13
644 648 6.545666 AGATAGATATAGATGAACCTCAGGCG 59.454 42.308 0.00 0.00 0.00 5.52
645 649 7.896383 AGATAGATATAGATGAACCTCAGGC 57.104 40.000 0.00 0.00 0.00 4.85
646 650 9.349713 GGTAGATAGATATAGATGAACCTCAGG 57.650 40.741 0.00 0.00 0.00 3.86
1169 2015 2.239654 CAGAGAGAGGTGAGAGAGGAGT 59.760 54.545 0.00 0.00 0.00 3.85
1514 2873 0.959867 CGACCACCAACCATGCATGA 60.960 55.000 28.31 0.00 0.00 3.07
1542 2901 1.903877 GCCACCTGCTGAAGCTCCTA 61.904 60.000 3.61 0.00 42.66 2.94
1584 2943 2.038689 TGCATTGGGGAACGTTGTACTA 59.961 45.455 5.00 0.00 0.00 1.82
2657 4360 4.730042 CGATGGTTTCGTTTTGATGCTATG 59.270 41.667 0.00 0.00 43.01 2.23
3085 4795 8.470657 AAGCTATAGATAGATGATAATGCGGA 57.529 34.615 3.21 0.00 32.05 5.54
4089 5891 9.128107 CATGCTTAGTTGTGTTTTGTAATTAGG 57.872 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.