Multiple sequence alignment - TraesCS6B01G322800

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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 TraesCS6B01G322800 chr6B 100.000 2237 0 0 1 2237 571760436 571758200 0.000000e+00 4132.0
1 TraesCS6B01G322800 chr6B 93.580 919 59 0 1319 2237 439015593 439014675 0.000000e+00 1371.0
2 TraesCS6B01G322800 chr6B 91.103 562 49 1 774 1334 567543556 567544117 0.000000e+00 760.0
3 TraesCS6B01G322800 chr2B 95.044 908 44 1 1331 2237 503636906 503637813 0.000000e+00 1426.0
4 TraesCS6B01G322800 chr2B 90.461 912 82 4 1330 2237 676189539 676188629 0.000000e+00 1197.0
5 TraesCS6B01G322800 chr1B 95.122 902 43 1 1337 2237 631059719 631058818 0.000000e+00 1421.0
6 TraesCS6B01G322800 chr1B 92.155 905 66 5 1336 2237 547576122 547575220 0.000000e+00 1273.0
7 TraesCS6B01G322800 chr1B 90.767 574 47 5 774 1343 381500990 381500419 0.000000e+00 761.0
8 TraesCS6B01G322800 chr1B 90.018 571 50 6 770 1336 198407730 198407163 0.000000e+00 732.0
9 TraesCS6B01G322800 chr3B 90.919 914 76 6 1330 2237 708796420 708795508 0.000000e+00 1221.0
10 TraesCS6B01G322800 chr3B 89.912 565 52 5 774 1336 700042836 700042275 0.000000e+00 723.0
11 TraesCS6B01G322800 chr3B 88.168 262 24 5 252 512 800092471 800092216 2.790000e-79 305.0
12 TraesCS6B01G322800 chr3B 100.000 30 0 0 451 480 575253982 575253953 3.100000e-04 56.5
13 TraesCS6B01G322800 chr5B 90.508 906 78 5 1336 2237 541101882 541102783 0.000000e+00 1190.0
14 TraesCS6B01G322800 chr5B 83.652 471 68 8 181 645 391443246 391443713 3.410000e-118 435.0
15 TraesCS6B01G322800 chr5B 74.031 516 87 39 152 652 478677601 478678084 1.370000e-37 167.0
16 TraesCS6B01G322800 chr4A 90.319 909 79 7 1331 2237 744463608 744462707 0.000000e+00 1182.0
17 TraesCS6B01G322800 chr6A 90.220 910 82 5 1334 2237 22757717 22756809 0.000000e+00 1181.0
18 TraesCS6B01G322800 chr6A 85.519 366 44 5 1 363 616222401 616222760 7.540000e-100 374.0
19 TraesCS6B01G322800 chr1A 90.989 566 45 4 775 1336 562118782 562118219 0.000000e+00 758.0
20 TraesCS6B01G322800 chr1D 90.941 563 49 2 774 1336 361102329 361101769 0.000000e+00 756.0
21 TraesCS6B01G322800 chr3A 90.829 567 46 3 775 1336 472765493 472764928 0.000000e+00 754.0
22 TraesCS6B01G322800 chr3A 79.372 223 36 9 152 365 532096111 532096332 4.980000e-32 148.0
23 TraesCS6B01G322800 chr3A 88.889 63 4 3 283 343 60514377 60514438 8.570000e-10 75.0
24 TraesCS6B01G322800 chr5D 90.586 563 53 0 774 1336 464405219 464405781 0.000000e+00 747.0
25 TraesCS6B01G322800 chr4B 90.459 566 44 6 774 1336 105359639 105359081 0.000000e+00 737.0
26 TraesCS6B01G322800 chr7B 88.479 434 40 6 4 433 59319708 59319281 1.180000e-142 516.0
27 TraesCS6B01G322800 chrUn 79.144 724 75 34 1 685 240896094 240896780 4.410000e-117 431.0
28 TraesCS6B01G322800 chrUn 86.687 323 34 7 192 512 41960204 41959889 1.270000e-92 350.0
29 TraesCS6B01G322800 chrUn 84.713 157 19 3 4 160 268927803 268927652 3.850000e-33 152.0
30 TraesCS6B01G322800 chr2D 84.375 128 15 3 4 131 537405418 537405296 1.090000e-23 121.0
31 TraesCS6B01G322800 chr2A 74.708 257 57 6 152 401 778452992 778452737 8.450000e-20 108.0


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 TraesCS6B01G322800 chr6B 571758200 571760436 2236 True 4132 4132 100.000 1 2237 1 chr6B.!!$R2 2236
1 TraesCS6B01G322800 chr6B 439014675 439015593 918 True 1371 1371 93.580 1319 2237 1 chr6B.!!$R1 918
2 TraesCS6B01G322800 chr6B 567543556 567544117 561 False 760 760 91.103 774 1334 1 chr6B.!!$F1 560
3 TraesCS6B01G322800 chr2B 503636906 503637813 907 False 1426 1426 95.044 1331 2237 1 chr2B.!!$F1 906
4 TraesCS6B01G322800 chr2B 676188629 676189539 910 True 1197 1197 90.461 1330 2237 1 chr2B.!!$R1 907
5 TraesCS6B01G322800 chr1B 631058818 631059719 901 True 1421 1421 95.122 1337 2237 1 chr1B.!!$R4 900
6 TraesCS6B01G322800 chr1B 547575220 547576122 902 True 1273 1273 92.155 1336 2237 1 chr1B.!!$R3 901
7 TraesCS6B01G322800 chr1B 381500419 381500990 571 True 761 761 90.767 774 1343 1 chr1B.!!$R2 569
8 TraesCS6B01G322800 chr1B 198407163 198407730 567 True 732 732 90.018 770 1336 1 chr1B.!!$R1 566
9 TraesCS6B01G322800 chr3B 708795508 708796420 912 True 1221 1221 90.919 1330 2237 1 chr3B.!!$R3 907
10 TraesCS6B01G322800 chr3B 700042275 700042836 561 True 723 723 89.912 774 1336 1 chr3B.!!$R2 562
11 TraesCS6B01G322800 chr5B 541101882 541102783 901 False 1190 1190 90.508 1336 2237 1 chr5B.!!$F3 901
12 TraesCS6B01G322800 chr4A 744462707 744463608 901 True 1182 1182 90.319 1331 2237 1 chr4A.!!$R1 906
13 TraesCS6B01G322800 chr6A 22756809 22757717 908 True 1181 1181 90.220 1334 2237 1 chr6A.!!$R1 903
14 TraesCS6B01G322800 chr1A 562118219 562118782 563 True 758 758 90.989 775 1336 1 chr1A.!!$R1 561
15 TraesCS6B01G322800 chr1D 361101769 361102329 560 True 756 756 90.941 774 1336 1 chr1D.!!$R1 562
16 TraesCS6B01G322800 chr3A 472764928 472765493 565 True 754 754 90.829 775 1336 1 chr3A.!!$R1 561
17 TraesCS6B01G322800 chr5D 464405219 464405781 562 False 747 747 90.586 774 1336 1 chr5D.!!$F1 562
18 TraesCS6B01G322800 chr4B 105359081 105359639 558 True 737 737 90.459 774 1336 1 chr4B.!!$R1 562
19 TraesCS6B01G322800 chrUn 240896094 240896780 686 False 431 431 79.144 1 685 1 chrUn.!!$F1 684

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
20 21 0.031616 AAGGGCAAACCAGGAAACCA 60.032 50.0 0.0 0.0 43.89 3.67 F
28 29 0.179029 ACCAGGAAACCACGACCAAG 60.179 55.0 0.0 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 1215 0.749454 GCCATCGCCCAAAGAGACAT 60.749 55.0 0.0 0.0 0.0 3.06 R
1590 1644 0.940519 CGAAGTGGGCGACGTGTTTA 60.941 55.0 0.0 0.0 0.0 2.01 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
20 21 0.031616 AAGGGCAAACCAGGAAACCA 60.032 50.000 0.00 0.00 43.89 3.67
28 29 0.179029 ACCAGGAAACCACGACCAAG 60.179 55.000 0.00 0.00 0.00 3.61
60 61 2.683933 GGGGAGGCGGAGAAGTGA 60.684 66.667 0.00 0.00 0.00 3.41
69 70 1.903877 CGGAGAAGTGACCCATGGCT 61.904 60.000 6.09 0.00 0.00 4.75
73 74 0.535335 GAAGTGACCCATGGCTACGA 59.465 55.000 6.09 0.00 0.00 3.43
78 79 3.467226 CCCATGGCTACGACCGGT 61.467 66.667 6.92 6.92 0.00 5.28
80 81 2.890474 CATGGCTACGACCGGTGC 60.890 66.667 14.63 9.45 0.00 5.01
124 125 1.519751 CCCCGAAACCATGTTTCGCA 61.520 55.000 27.59 0.00 46.89 5.10
128 129 0.958822 GAAACCATGTTTCGCACCCT 59.041 50.000 4.16 0.00 0.00 4.34
150 151 2.867109 CCGAAGGCCCAGATATGATT 57.133 50.000 0.00 0.00 46.14 2.57
201 203 2.815211 CGCCACGCTGCAGTACAT 60.815 61.111 16.64 0.00 0.00 2.29
202 204 2.787249 GCCACGCTGCAGTACATG 59.213 61.111 16.64 8.46 0.00 3.21
208 210 2.817423 GCTGCAGTACATGAGCCGC 61.817 63.158 16.64 2.38 0.00 6.53
266 300 4.900154 GGAGACGCCACAGAGAAG 57.100 61.111 0.00 0.00 36.34 2.85
294 328 2.203625 GCCTGCCCAAACCCAGAA 60.204 61.111 0.00 0.00 0.00 3.02
315 350 4.894719 CCCAAAAGGGCCCAGATT 57.105 55.556 27.56 13.45 34.21 2.40
378 413 2.591429 CAAGCAGCCACACCGTCA 60.591 61.111 0.00 0.00 0.00 4.35
506 541 2.609921 GGGGGAGGAAGAACGGGT 60.610 66.667 0.00 0.00 0.00 5.28
535 570 2.730094 GGCACCACACAAGCAAGG 59.270 61.111 0.00 0.00 0.00 3.61
551 586 3.468140 GGCCCGGTGGTCTAGGTC 61.468 72.222 0.00 0.00 31.67 3.85
552 587 3.834799 GCCCGGTGGTCTAGGTCG 61.835 72.222 0.00 0.00 0.00 4.79
553 588 2.044650 CCCGGTGGTCTAGGTCGA 60.045 66.667 0.00 0.00 0.00 4.20
554 589 2.413142 CCCGGTGGTCTAGGTCGAC 61.413 68.421 7.13 7.13 0.00 4.20
555 590 2.758089 CCGGTGGTCTAGGTCGACG 61.758 68.421 9.92 0.00 34.75 5.12
556 591 2.758089 CGGTGGTCTAGGTCGACGG 61.758 68.421 9.92 2.47 34.75 4.79
557 592 2.488820 GTGGTCTAGGTCGACGGC 59.511 66.667 9.92 0.00 34.75 5.68
558 593 3.129502 TGGTCTAGGTCGACGGCG 61.130 66.667 2.87 2.87 34.75 6.46
559 594 3.885521 GGTCTAGGTCGACGGCGG 61.886 72.222 12.58 0.00 38.28 6.13
560 595 4.549516 GTCTAGGTCGACGGCGGC 62.550 72.222 12.58 9.84 42.49 6.53
578 613 4.364686 GGGAGGGGAAGGTGGGGA 62.365 72.222 0.00 0.00 0.00 4.81
579 614 2.692741 GGAGGGGAAGGTGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
580 615 2.454941 GAGGGGAAGGTGGGGAGA 59.545 66.667 0.00 0.00 0.00 3.71
581 616 1.690985 GAGGGGAAGGTGGGGAGAG 60.691 68.421 0.00 0.00 0.00 3.20
582 617 2.692741 GGGGAAGGTGGGGAGAGG 60.693 72.222 0.00 0.00 0.00 3.69
583 618 2.692741 GGGAAGGTGGGGAGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
584 619 2.692741 GGAAGGTGGGGAGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
585 620 2.692741 GAAGGTGGGGAGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
593 628 4.741239 GGAGAGGGGGCACTGGGA 62.741 72.222 0.00 0.00 0.00 4.37
594 629 3.086600 GAGAGGGGGCACTGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
595 630 4.748798 AGAGGGGGCACTGGGAGG 62.749 72.222 0.00 0.00 0.00 4.30
627 662 4.090588 CCCCGGTTGCCTCGCTTA 62.091 66.667 0.00 0.00 0.00 3.09
628 663 2.511600 CCCGGTTGCCTCGCTTAG 60.512 66.667 0.00 0.00 0.00 2.18
630 665 2.511600 CGGTTGCCTCGCTTAGGG 60.512 66.667 4.33 0.00 46.65 3.53
631 666 2.987125 GGTTGCCTCGCTTAGGGA 59.013 61.111 0.00 0.00 46.65 4.20
641 676 4.570663 CTTAGGGAGGCGACGCGG 62.571 72.222 14.61 0.00 0.00 6.46
657 692 4.837421 GGGGGTACAGGGGAGGGG 62.837 77.778 0.00 0.00 0.00 4.79
658 693 4.837421 GGGGTACAGGGGAGGGGG 62.837 77.778 0.00 0.00 0.00 5.40
659 694 3.702623 GGGTACAGGGGAGGGGGA 61.703 72.222 0.00 0.00 0.00 4.81
660 695 2.457794 GGTACAGGGGAGGGGGAA 59.542 66.667 0.00 0.00 0.00 3.97
661 696 1.693103 GGTACAGGGGAGGGGGAAG 60.693 68.421 0.00 0.00 0.00 3.46
662 697 1.693103 GTACAGGGGAGGGGGAAGG 60.693 68.421 0.00 0.00 0.00 3.46
663 698 2.968462 TACAGGGGAGGGGGAAGGG 61.968 68.421 0.00 0.00 0.00 3.95
666 701 4.845307 GGGGAGGGGGAAGGGGAG 62.845 77.778 0.00 0.00 0.00 4.30
667 702 3.707189 GGGAGGGGGAAGGGGAGA 61.707 72.222 0.00 0.00 0.00 3.71
668 703 2.040359 GGAGGGGGAAGGGGAGAG 60.040 72.222 0.00 0.00 0.00 3.20
669 704 2.040359 GAGGGGGAAGGGGAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
670 705 3.711782 AGGGGGAAGGGGAGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
671 706 4.845307 GGGGGAAGGGGAGAGGGG 62.845 77.778 0.00 0.00 0.00 4.79
672 707 3.707189 GGGGAAGGGGAGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
673 708 2.040359 GGGAAGGGGAGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
674 709 2.040359 GGAAGGGGAGAGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
675 710 2.040359 GAAGGGGAGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
676 711 2.882143 AAGGGGAGAGGGGAGGGT 60.882 66.667 0.00 0.00 0.00 4.34
677 712 2.494151 GAAGGGGAGAGGGGAGGGTT 62.494 65.000 0.00 0.00 0.00 4.11
678 713 2.692741 GGGGAGAGGGGAGGGTTG 60.693 72.222 0.00 0.00 0.00 3.77
679 714 2.692741 GGGAGAGGGGAGGGTTGG 60.693 72.222 0.00 0.00 0.00 3.77
680 715 2.692741 GGAGAGGGGAGGGTTGGG 60.693 72.222 0.00 0.00 0.00 4.12
681 716 2.125225 GAGAGGGGAGGGTTGGGT 59.875 66.667 0.00 0.00 0.00 4.51
682 717 2.204151 AGAGGGGAGGGTTGGGTG 60.204 66.667 0.00 0.00 0.00 4.61
683 718 2.204090 GAGGGGAGGGTTGGGTGA 60.204 66.667 0.00 0.00 0.00 4.02
684 719 2.204151 AGGGGAGGGTTGGGTGAG 60.204 66.667 0.00 0.00 0.00 3.51
685 720 4.048470 GGGGAGGGTTGGGTGAGC 62.048 72.222 0.00 0.00 0.00 4.26
686 721 3.256960 GGGAGGGTTGGGTGAGCA 61.257 66.667 0.00 0.00 0.00 4.26
687 722 2.352805 GGAGGGTTGGGTGAGCAG 59.647 66.667 0.00 0.00 0.00 4.24
688 723 2.360475 GAGGGTTGGGTGAGCAGC 60.360 66.667 0.00 0.00 0.00 5.25
689 724 4.335647 AGGGTTGGGTGAGCAGCG 62.336 66.667 0.00 0.00 0.00 5.18
690 725 4.329545 GGGTTGGGTGAGCAGCGA 62.330 66.667 0.00 0.00 0.00 4.93
691 726 3.050275 GGTTGGGTGAGCAGCGAC 61.050 66.667 0.00 0.00 0.00 5.19
692 727 3.414700 GTTGGGTGAGCAGCGACG 61.415 66.667 0.00 0.00 0.00 5.12
693 728 4.680237 TTGGGTGAGCAGCGACGG 62.680 66.667 0.00 0.00 0.00 4.79
743 778 2.908796 GGCGAAACCCTAGGGAGG 59.091 66.667 35.38 19.31 43.33 4.30
768 803 4.143333 GCGGCGGAGACCTTGCTA 62.143 66.667 9.78 0.00 0.00 3.49
769 804 2.105128 CGGCGGAGACCTTGCTAG 59.895 66.667 0.00 0.00 0.00 3.42
771 806 2.058595 GGCGGAGACCTTGCTAGGA 61.059 63.158 21.63 0.00 45.05 2.94
772 807 1.614241 GGCGGAGACCTTGCTAGGAA 61.614 60.000 21.63 0.00 45.05 3.36
804 842 1.780503 AGTTCTTTGCCTGGCTTGTT 58.219 45.000 21.03 0.00 0.00 2.83
908 946 1.026718 CAAGAGTCGGCCAACCATCC 61.027 60.000 2.24 0.00 34.57 3.51
935 973 2.901281 AATGCCGCTACACCACCCA 61.901 57.895 0.00 0.00 0.00 4.51
956 994 8.960591 CACCCACATTTAGAACAATATTCTTCT 58.039 33.333 10.35 10.35 0.00 2.85
1038 1076 1.104577 GGTGGAACGGCAACCTTCAA 61.105 55.000 0.00 0.00 38.12 2.69
1043 1081 3.637229 TGGAACGGCAACCTTCAAATTTA 59.363 39.130 0.00 0.00 0.00 1.40
1051 1089 4.988540 GCAACCTTCAAATTTACCTTGGAC 59.011 41.667 0.00 0.00 0.00 4.02
1134 1172 4.415881 TGCCAGAGTCTTTAGAAACACA 57.584 40.909 0.00 0.00 0.00 3.72
1142 1180 4.042187 AGTCTTTAGAAACACAGCCATCCT 59.958 41.667 0.00 0.00 0.00 3.24
1152 1190 1.026718 CAGCCATCCTTTCCACGGTC 61.027 60.000 0.00 0.00 0.00 4.79
1174 1212 6.273825 GTCCTAATCAGTAAGATCAAAGCGA 58.726 40.000 0.00 0.00 35.39 4.93
1177 1215 6.980978 CCTAATCAGTAAGATCAAAGCGAAGA 59.019 38.462 0.00 0.00 35.39 2.87
1302 1353 8.855110 TGTTTGCAACTTCCTTCTTAATCAATA 58.145 29.630 0.00 0.00 0.00 1.90
1384 1436 1.404181 CGTTCACCATCTCGACCACAT 60.404 52.381 0.00 0.00 0.00 3.21
1908 2014 1.961277 GGCGATTCGGCGATGGATT 60.961 57.895 17.13 0.00 43.33 3.01
1919 2025 1.358725 CGATGGATTGGTGTTCGCGT 61.359 55.000 5.77 0.00 0.00 6.01
1954 2060 0.375803 GTGCTTGTCGTTTTCGGTGT 59.624 50.000 0.00 0.00 44.25 4.16
2129 2235 4.141642 GGGGAGAATTTTGGGGATGAATTG 60.142 45.833 0.00 0.00 0.00 2.32
2190 2297 7.753580 AGTTAGTTGTTTTTCAAACTGCAGTAC 59.246 33.333 22.01 13.20 37.81 2.73
2200 2307 2.185004 ACTGCAGTACGAAGGCAAAT 57.815 45.000 20.16 0.00 37.06 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.385528 GGTTGACTTGGTCGTGGTTT 58.614 50.000 0.00 0.00 34.95 3.27
20 21 2.424302 CCCGGTTGACTTGGTCGT 59.576 61.111 0.00 0.00 34.95 4.34
28 29 2.035155 CCCTTTCCCCCGGTTGAC 59.965 66.667 0.00 0.00 0.00 3.18
60 61 3.467226 CCGGTCGTAGCCATGGGT 61.467 66.667 22.15 22.15 0.00 4.51
69 70 4.367023 GCACAGGCACCGGTCGTA 62.367 66.667 2.59 0.00 40.72 3.43
104 105 1.880186 CGAAACATGGTTTCGGGGG 59.120 57.895 27.42 7.83 45.17 5.40
112 113 1.671054 CGAGGGTGCGAAACATGGT 60.671 57.895 0.00 0.00 0.00 3.55
139 140 1.446907 GCTCGGCCAATCATATCTGG 58.553 55.000 2.24 0.00 35.67 3.86
186 188 1.699656 GCTCATGTACTGCAGCGTGG 61.700 60.000 15.27 5.78 0.00 4.94
188 190 1.448540 GGCTCATGTACTGCAGCGT 60.449 57.895 15.27 0.00 32.23 5.07
245 279 1.226802 CTCTGTGGCGTCTCCGATG 60.227 63.158 0.00 0.00 37.80 3.84
246 280 0.965866 TTCTCTGTGGCGTCTCCGAT 60.966 55.000 0.00 0.00 37.80 4.18
247 281 1.587043 CTTCTCTGTGGCGTCTCCGA 61.587 60.000 0.00 0.00 37.80 4.55
258 292 2.604686 TGGCCGGAGCTTCTCTGT 60.605 61.111 5.05 0.00 39.73 3.41
260 294 3.080121 CCTGGCCGGAGCTTCTCT 61.080 66.667 15.09 0.00 39.73 3.10
489 524 2.609921 ACCCGTTCTTCCTCCCCC 60.610 66.667 0.00 0.00 0.00 5.40
494 529 3.703127 GGCGGACCCGTTCTTCCT 61.703 66.667 10.37 0.00 42.09 3.36
516 551 3.829272 CTTGCTTGTGTGGTGCCGC 62.829 63.158 0.00 0.00 0.00 6.53
518 553 2.730094 CCTTGCTTGTGTGGTGCC 59.270 61.111 0.00 0.00 0.00 5.01
528 563 4.660938 GACCACCGGGCCTTGCTT 62.661 66.667 6.32 0.00 37.90 3.91
535 570 3.834799 CGACCTAGACCACCGGGC 61.835 72.222 6.32 0.00 37.90 6.13
561 596 4.364686 TCCCCACCTTCCCCTCCC 62.365 72.222 0.00 0.00 0.00 4.30
562 597 2.692741 CTCCCCACCTTCCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
563 598 1.690985 CTCTCCCCACCTTCCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
564 599 2.456840 CTCTCCCCACCTTCCCCT 59.543 66.667 0.00 0.00 0.00 4.79
565 600 2.692741 CCTCTCCCCACCTTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
566 601 2.692741 CCCTCTCCCCACCTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
567 602 2.692741 CCCCTCTCCCCACCTTCC 60.693 72.222 0.00 0.00 0.00 3.46
568 603 2.692741 CCCCCTCTCCCCACCTTC 60.693 72.222 0.00 0.00 0.00 3.46
576 611 4.741239 TCCCAGTGCCCCCTCTCC 62.741 72.222 0.00 0.00 0.00 3.71
577 612 3.086600 CTCCCAGTGCCCCCTCTC 61.087 72.222 0.00 0.00 0.00 3.20
578 613 4.748798 CCTCCCAGTGCCCCCTCT 62.749 72.222 0.00 0.00 0.00 3.69
610 645 4.090588 TAAGCGAGGCAACCGGGG 62.091 66.667 6.32 0.00 37.17 5.73
611 646 2.511600 CTAAGCGAGGCAACCGGG 60.512 66.667 6.32 0.00 37.17 5.73
612 647 2.511600 CCTAAGCGAGGCAACCGG 60.512 66.667 0.00 0.00 38.96 5.28
613 648 2.511600 CCCTAAGCGAGGCAACCG 60.512 66.667 2.28 0.00 45.17 4.44
614 649 1.153349 CTCCCTAAGCGAGGCAACC 60.153 63.158 2.28 0.00 45.17 3.77
615 650 1.153349 CCTCCCTAAGCGAGGCAAC 60.153 63.158 2.28 0.00 45.17 4.17
616 651 3.309582 CCTCCCTAAGCGAGGCAA 58.690 61.111 2.28 0.00 45.17 4.52
624 659 4.570663 CCGCGTCGCCTCCCTAAG 62.571 72.222 12.44 0.00 0.00 2.18
640 675 4.837421 CCCCTCCCCTGTACCCCC 62.837 77.778 0.00 0.00 0.00 5.40
641 676 4.837421 CCCCCTCCCCTGTACCCC 62.837 77.778 0.00 0.00 0.00 4.95
642 677 3.277514 TTCCCCCTCCCCTGTACCC 62.278 68.421 0.00 0.00 0.00 3.69
643 678 1.693103 CTTCCCCCTCCCCTGTACC 60.693 68.421 0.00 0.00 0.00 3.34
644 679 1.693103 CCTTCCCCCTCCCCTGTAC 60.693 68.421 0.00 0.00 0.00 2.90
645 680 2.792222 CCTTCCCCCTCCCCTGTA 59.208 66.667 0.00 0.00 0.00 2.74
646 681 4.371231 CCCTTCCCCCTCCCCTGT 62.371 72.222 0.00 0.00 0.00 4.00
649 684 4.845307 CTCCCCTTCCCCCTCCCC 62.845 77.778 0.00 0.00 0.00 4.81
650 685 3.707189 TCTCCCCTTCCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
651 686 2.040359 CTCTCCCCTTCCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
652 687 2.040359 CCTCTCCCCTTCCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
653 688 3.711782 CCCTCTCCCCTTCCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
654 689 4.845307 CCCCTCTCCCCTTCCCCC 62.845 77.778 0.00 0.00 0.00 5.40
655 690 3.707189 TCCCCTCTCCCCTTCCCC 61.707 72.222 0.00 0.00 0.00 4.81
656 691 2.040359 CTCCCCTCTCCCCTTCCC 60.040 72.222 0.00 0.00 0.00 3.97
657 692 2.040359 CCTCCCCTCTCCCCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
658 693 2.040359 CCCTCCCCTCTCCCCTTC 60.040 72.222 0.00 0.00 0.00 3.46
659 694 2.511458 AACCCTCCCCTCTCCCCTT 61.511 63.158 0.00 0.00 0.00 3.95
660 695 2.882143 AACCCTCCCCTCTCCCCT 60.882 66.667 0.00 0.00 0.00 4.79
661 696 2.692741 CAACCCTCCCCTCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
662 697 2.692741 CCAACCCTCCCCTCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
663 698 2.692741 CCCAACCCTCCCCTCTCC 60.693 72.222 0.00 0.00 0.00 3.71
664 699 2.125225 ACCCAACCCTCCCCTCTC 59.875 66.667 0.00 0.00 0.00 3.20
665 700 2.204151 CACCCAACCCTCCCCTCT 60.204 66.667 0.00 0.00 0.00 3.69
666 701 2.204090 TCACCCAACCCTCCCCTC 60.204 66.667 0.00 0.00 0.00 4.30
667 702 2.204151 CTCACCCAACCCTCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
668 703 4.048470 GCTCACCCAACCCTCCCC 62.048 72.222 0.00 0.00 0.00 4.81
669 704 3.256960 TGCTCACCCAACCCTCCC 61.257 66.667 0.00 0.00 0.00 4.30
670 705 2.352805 CTGCTCACCCAACCCTCC 59.647 66.667 0.00 0.00 0.00 4.30
671 706 2.360475 GCTGCTCACCCAACCCTC 60.360 66.667 0.00 0.00 0.00 4.30
672 707 4.335647 CGCTGCTCACCCAACCCT 62.336 66.667 0.00 0.00 0.00 4.34
673 708 4.329545 TCGCTGCTCACCCAACCC 62.330 66.667 0.00 0.00 0.00 4.11
674 709 3.050275 GTCGCTGCTCACCCAACC 61.050 66.667 0.00 0.00 0.00 3.77
675 710 3.414700 CGTCGCTGCTCACCCAAC 61.415 66.667 0.00 0.00 0.00 3.77
676 711 4.680237 CCGTCGCTGCTCACCCAA 62.680 66.667 0.00 0.00 0.00 4.12
726 761 2.908796 CCTCCCTAGGGTTTCGCC 59.091 66.667 27.58 0.00 39.48 5.54
751 786 4.143333 TAGCAAGGTCTCCGCCGC 62.143 66.667 0.00 0.00 0.00 6.53
752 787 2.105128 CTAGCAAGGTCTCCGCCG 59.895 66.667 0.00 0.00 0.00 6.46
753 788 1.614241 TTCCTAGCAAGGTCTCCGCC 61.614 60.000 0.00 0.00 44.09 6.13
754 789 0.460459 GTTCCTAGCAAGGTCTCCGC 60.460 60.000 0.00 0.00 44.09 5.54
755 790 0.175989 GGTTCCTAGCAAGGTCTCCG 59.824 60.000 0.00 0.00 44.09 4.63
756 791 0.542333 GGGTTCCTAGCAAGGTCTCC 59.458 60.000 0.00 0.00 44.09 3.71
757 792 0.542333 GGGGTTCCTAGCAAGGTCTC 59.458 60.000 0.00 0.00 44.09 3.36
758 793 0.178873 TGGGGTTCCTAGCAAGGTCT 60.179 55.000 0.00 0.00 44.09 3.85
759 794 0.696501 TTGGGGTTCCTAGCAAGGTC 59.303 55.000 0.00 0.00 44.09 3.85
760 795 0.698818 CTTGGGGTTCCTAGCAAGGT 59.301 55.000 0.00 0.00 44.09 3.50
761 796 0.034089 CCTTGGGGTTCCTAGCAAGG 60.034 60.000 9.34 9.34 45.21 3.61
762 797 0.698818 ACCTTGGGGTTCCTAGCAAG 59.301 55.000 0.00 0.00 44.73 4.01
763 798 0.404040 CACCTTGGGGTTCCTAGCAA 59.596 55.000 0.00 0.00 44.73 3.91
764 799 2.074967 CACCTTGGGGTTCCTAGCA 58.925 57.895 0.00 0.00 44.73 3.49
765 800 1.378646 GCACCTTGGGGTTCCTAGC 60.379 63.158 0.00 0.00 44.73 3.42
766 801 0.404040 TTGCACCTTGGGGTTCCTAG 59.596 55.000 0.00 0.00 44.73 3.02
767 802 0.404040 CTTGCACCTTGGGGTTCCTA 59.596 55.000 0.00 0.00 44.73 2.94
768 803 1.153756 CTTGCACCTTGGGGTTCCT 59.846 57.895 0.00 0.00 44.73 3.36
769 804 0.759060 AACTTGCACCTTGGGGTTCC 60.759 55.000 0.00 0.00 44.73 3.62
770 805 0.673985 GAACTTGCACCTTGGGGTTC 59.326 55.000 0.00 0.00 44.73 3.62
771 806 0.261696 AGAACTTGCACCTTGGGGTT 59.738 50.000 0.00 0.00 44.73 4.11
804 842 6.318648 CCGATGTCCAAATCCTATTTTGAAGA 59.681 38.462 0.00 0.00 38.58 2.87
902 940 1.571955 GCATTGGAAAAGGGGATGGT 58.428 50.000 0.00 0.00 0.00 3.55
908 946 0.455815 GTAGCGGCATTGGAAAAGGG 59.544 55.000 1.45 0.00 0.00 3.95
956 994 3.015675 TGTGATGCATTCCAAGCCATA 57.984 42.857 0.00 0.00 0.00 2.74
957 995 1.855295 TGTGATGCATTCCAAGCCAT 58.145 45.000 0.00 0.00 0.00 4.40
1038 1076 3.271225 CCTTAGGGGGTCCAAGGTAAATT 59.729 47.826 0.00 0.00 36.96 1.82
1043 1081 1.929088 GCCTTAGGGGGTCCAAGGT 60.929 63.158 0.00 0.00 40.41 3.50
1072 1110 6.705302 TCTCCCATGAGATAAGCATCATAAC 58.295 40.000 0.00 0.00 42.73 1.89
1104 1142 1.479709 AGACTCTGGCATTACGCTCT 58.520 50.000 0.00 0.00 41.91 4.09
1125 1163 3.073798 TGGAAAGGATGGCTGTGTTTCTA 59.926 43.478 0.00 0.00 0.00 2.10
1134 1172 1.299976 GACCGTGGAAAGGATGGCT 59.700 57.895 0.00 0.00 37.88 4.75
1142 1180 4.773674 TCTTACTGATTAGGACCGTGGAAA 59.226 41.667 0.00 0.00 0.00 3.13
1152 1190 6.980978 TCTTCGCTTTGATCTTACTGATTAGG 59.019 38.462 0.00 0.00 35.14 2.69
1177 1215 0.749454 GCCATCGCCCAAAGAGACAT 60.749 55.000 0.00 0.00 0.00 3.06
1207 1245 2.675844 GCGGCATTACAACACTCATGTA 59.324 45.455 0.00 0.00 38.45 2.29
1266 1315 3.376218 TTGCAAACAAAAGCCGCAT 57.624 42.105 0.00 0.00 31.21 4.73
1384 1436 1.078497 GTGGACGGTGATGGATGCA 60.078 57.895 0.00 0.00 0.00 3.96
1590 1644 0.940519 CGAAGTGGGCGACGTGTTTA 60.941 55.000 0.00 0.00 0.00 2.01
1905 2011 2.776072 CCGACGCGAACACCAATC 59.224 61.111 15.93 0.00 0.00 2.67
1954 2060 1.300620 CGACGAAACTGCCCAGTGA 60.301 57.895 1.07 0.00 41.58 3.41
2129 2235 4.635765 TCAATGGCAACTATAGTGACTTGC 59.364 41.667 15.86 15.86 37.61 4.01
2190 2297 3.252215 TCAAACTACCACATTTGCCTTCG 59.748 43.478 0.00 0.00 36.06 3.79
2200 2307 5.464057 CGTGACATTTACTCAAACTACCACA 59.536 40.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.