Multiple sequence alignment - TraesCS4D01G333100

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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 TraesCS4D01G333100 chr4D 100.000 3818 0 0 1 3818 490406297 490402480 0.000000e+00 7051.0
1 TraesCS4D01G333100 chr4D 81.105 2117 294 56 950 3040 490413490 490411454 0.000000e+00 1596.0
2 TraesCS4D01G333100 chr4D 79.470 755 114 22 3070 3818 490377754 490378473 7.370000e-137 497.0
3 TraesCS4D01G333100 chr4D 81.270 630 97 15 3105 3728 490411253 490410639 1.230000e-134 490.0
4 TraesCS4D01G333100 chr4D 80.139 433 69 5 1696 2112 490375966 490376397 1.330000e-79 307.0
5 TraesCS4D01G333100 chr4B 95.370 2894 109 11 946 3818 630015962 630013073 0.000000e+00 4578.0
6 TraesCS4D01G333100 chr4B 82.117 1124 142 32 979 2070 630099923 630098827 0.000000e+00 907.0
7 TraesCS4D01G333100 chr4B 79.076 1386 209 47 1689 3040 630043735 630042397 0.000000e+00 878.0
8 TraesCS4D01G333100 chr4B 81.564 857 112 23 2072 2914 630098742 630097918 0.000000e+00 665.0
9 TraesCS4D01G333100 chr4B 84.164 682 73 11 950 1629 630044711 630044063 2.500000e-176 628.0
10 TraesCS4D01G333100 chr4B 82.019 723 98 20 3105 3818 630042112 630041413 1.530000e-163 586.0
11 TraesCS4D01G333100 chr4B 90.000 390 38 1 140 529 591925580 591925192 1.580000e-138 503.0
12 TraesCS4D01G333100 chr4B 86.667 255 27 2 598 851 591925195 591924947 3.760000e-70 276.0
13 TraesCS4D01G333100 chr5A 92.401 3040 147 29 838 3818 671978946 671975932 0.000000e+00 4257.0
14 TraesCS4D01G333100 chr5A 79.972 1448 198 40 1608 3040 672028049 672026679 0.000000e+00 983.0
15 TraesCS4D01G333100 chr5A 88.696 805 59 5 1 786 671983141 671982350 0.000000e+00 953.0
16 TraesCS4D01G333100 chr5A 80.421 950 138 25 1285 2207 671955003 671955931 0.000000e+00 680.0
17 TraesCS4D01G333100 chr5A 84.858 667 66 10 950 1611 671990681 671990045 1.160000e-179 640.0
18 TraesCS4D01G333100 chr5A 87.115 520 33 10 83 572 451012995 451012480 3.330000e-155 558.0
19 TraesCS4D01G333100 chr5A 81.905 630 93 14 3105 3728 671988135 671987521 2.630000e-141 512.0
20 TraesCS4D01G333100 chr5A 79.576 754 114 20 3070 3817 671957212 671957931 1.580000e-138 503.0
21 TraesCS4D01G333100 chr5A 83.363 559 69 11 2491 3040 671988883 671988340 2.650000e-136 496.0
22 TraesCS4D01G333100 chr5A 83.370 457 51 10 112 556 181667498 181667055 2.140000e-107 399.0
23 TraesCS4D01G333100 chr5A 85.455 385 43 9 973 1352 672028574 672028198 4.630000e-104 388.0
24 TraesCS4D01G333100 chr5B 84.328 670 76 16 964 1629 505779528 505778884 2.500000e-176 628.0
25 TraesCS4D01G333100 chr5B 87.621 517 33 9 83 572 411544937 411544425 4.280000e-159 571.0
26 TraesCS4D01G333100 chr5B 87.838 74 9 0 26 99 411545033 411544960 1.890000e-13 87.9
27 TraesCS4D01G333100 chr1A 88.184 457 30 8 112 556 45252570 45253014 1.220000e-144 523.0
28 TraesCS4D01G333100 chr1A 87.295 244 21 5 614 855 45253007 45253242 1.750000e-68 270.0
29 TraesCS4D01G333100 chr1A 83.000 200 17 8 264 461 107460498 107460682 8.490000e-37 165.0
30 TraesCS4D01G333100 chr3B 87.033 455 35 6 112 554 168698985 168699427 3.430000e-135 492.0
31 TraesCS4D01G333100 chr3B 88.919 370 31 4 483 851 6976040 6975680 7.520000e-122 448.0
32 TraesCS4D01G333100 chr5D 83.939 523 29 20 83 572 350593661 350593161 2.090000e-122 449.0
33 TraesCS4D01G333100 chr2D 85.012 427 26 9 142 556 440616281 440615881 2.140000e-107 399.0
34 TraesCS4D01G333100 chr2D 88.559 236 20 2 617 851 440615885 440615656 2.900000e-71 279.0
35 TraesCS4D01G333100 chr6D 94.969 159 8 0 424 582 448660479 448660321 2.280000e-62 250.0
36 TraesCS4D01G333100 chr1D 85.892 241 24 5 614 851 290413386 290413619 8.190000e-62 248.0
37 TraesCS4D01G333100 chr1D 96.078 102 4 0 455 556 290413292 290413393 2.360000e-37 167.0
38 TraesCS4D01G333100 chr6A 83.770 191 21 5 664 851 7192370 7192187 5.070000e-39 172.0
39 TraesCS4D01G333100 chr6A 95.122 41 2 0 627 667 7192872 7192832 8.850000e-07 65.8
40 TraesCS4D01G333100 chr7B 82.447 188 22 7 664 847 567634395 567634575 1.840000e-33 154.0
41 TraesCS4D01G333100 chr6B 87.692 130 14 2 1079 1207 75671048 75670920 2.380000e-32 150.0
42 TraesCS4D01G333100 chr6B 81.481 189 22 9 664 847 84924998 84925178 3.980000e-30 143.0
43 TraesCS4D01G333100 chr6B 84.746 59 9 0 1400 1458 7823861 7823803 4.120000e-05 60.2
44 TraesCS4D01G333100 chr3D 93.617 47 3 0 627 673 610930897 610930851 1.900000e-08 71.3
45 TraesCS4D01G333100 chr2B 93.023 43 3 0 2730 2772 668033236 668033194 3.180000e-06 63.9


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 TraesCS4D01G333100 chr4D 490402480 490406297 3817 True 7051.000000 7051 100.000000 1 3818 1 chr4D.!!$R1 3817
1 TraesCS4D01G333100 chr4D 490410639 490413490 2851 True 1043.000000 1596 81.187500 950 3728 2 chr4D.!!$R2 2778
2 TraesCS4D01G333100 chr4D 490375966 490378473 2507 False 402.000000 497 79.804500 1696 3818 2 chr4D.!!$F1 2122
3 TraesCS4D01G333100 chr4B 630013073 630015962 2889 True 4578.000000 4578 95.370000 946 3818 1 chr4B.!!$R1 2872
4 TraesCS4D01G333100 chr4B 630097918 630099923 2005 True 786.000000 907 81.840500 979 2914 2 chr4B.!!$R4 1935
5 TraesCS4D01G333100 chr4B 630041413 630044711 3298 True 697.333333 878 81.753000 950 3818 3 chr4B.!!$R3 2868
6 TraesCS4D01G333100 chr4B 591924947 591925580 633 True 389.500000 503 88.333500 140 851 2 chr4B.!!$R2 711
7 TraesCS4D01G333100 chr5A 671975932 671983141 7209 True 2605.000000 4257 90.548500 1 3818 2 chr5A.!!$R3 3817
8 TraesCS4D01G333100 chr5A 672026679 672028574 1895 True 685.500000 983 82.713500 973 3040 2 chr5A.!!$R5 2067
9 TraesCS4D01G333100 chr5A 671955003 671957931 2928 False 591.500000 680 79.998500 1285 3817 2 chr5A.!!$F1 2532
10 TraesCS4D01G333100 chr5A 451012480 451012995 515 True 558.000000 558 87.115000 83 572 1 chr5A.!!$R2 489
11 TraesCS4D01G333100 chr5A 671987521 671990681 3160 True 549.333333 640 83.375333 950 3728 3 chr5A.!!$R4 2778
12 TraesCS4D01G333100 chr5B 505778884 505779528 644 True 628.000000 628 84.328000 964 1629 1 chr5B.!!$R1 665
13 TraesCS4D01G333100 chr5B 411544425 411545033 608 True 329.450000 571 87.729500 26 572 2 chr5B.!!$R2 546
14 TraesCS4D01G333100 chr1A 45252570 45253242 672 False 396.500000 523 87.739500 112 855 2 chr1A.!!$F2 743
15 TraesCS4D01G333100 chr5D 350593161 350593661 500 True 449.000000 449 83.939000 83 572 1 chr5D.!!$R1 489
16 TraesCS4D01G333100 chr2D 440615656 440616281 625 True 339.000000 399 86.785500 142 851 2 chr2D.!!$R1 709

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
746 889 0.039035 GGTGGTGATGGCTGGGTAAA 59.961 55.000 0.0 0.0 0.00 2.01 F
758 902 0.759959 TGGGTAAAGGCAACGAGTGA 59.240 50.000 0.0 0.0 46.39 3.41 F
920 4435 2.310538 GCCCATCAGTCCCCATTTTAG 58.689 52.381 0.0 0.0 0.00 1.85 F
2686 6898 1.280998 CCCCATTCCTACCTTTGTCGT 59.719 52.381 0.0 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 5682 0.615331 GATCACCACAAGGCTCTGGA 59.385 55.000 16.15 0.00 39.06 3.86 R
1817 5745 1.204941 CGAGAAAGGACCAGTGGTAGG 59.795 57.143 16.72 0.00 35.25 3.18 R
2775 6995 0.034756 CACCATCTCGACCACCAACA 59.965 55.000 0.00 0.00 0.00 3.33 R
3603 8247 2.317609 ACGCTTGCGGTTACAGCAG 61.318 57.895 19.19 6.45 46.01 4.24 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
72 73 1.207329 GGTACCTCTTCGTGATTGCCT 59.793 52.381 4.06 0.00 0.00 4.75
180 244 1.930204 TGGAGTCCCTGATCCAGTCTA 59.070 52.381 6.74 0.00 40.70 2.59
181 245 2.520120 TGGAGTCCCTGATCCAGTCTAT 59.480 50.000 6.74 0.00 40.70 1.98
453 529 4.479993 GAGAGCAGTGCGGGGCAT 62.480 66.667 10.00 0.00 41.91 4.40
574 650 3.330720 GGTGGAGTGGGGTGGGAG 61.331 72.222 0.00 0.00 0.00 4.30
575 651 2.529389 GTGGAGTGGGGTGGGAGT 60.529 66.667 0.00 0.00 0.00 3.85
576 652 1.229400 GTGGAGTGGGGTGGGAGTA 60.229 63.158 0.00 0.00 0.00 2.59
577 653 0.620700 GTGGAGTGGGGTGGGAGTAT 60.621 60.000 0.00 0.00 0.00 2.12
578 654 0.620410 TGGAGTGGGGTGGGAGTATG 60.620 60.000 0.00 0.00 0.00 2.39
579 655 1.345715 GGAGTGGGGTGGGAGTATGG 61.346 65.000 0.00 0.00 0.00 2.74
580 656 1.307866 AGTGGGGTGGGAGTATGGG 60.308 63.158 0.00 0.00 0.00 4.00
581 657 1.307517 GTGGGGTGGGAGTATGGGA 60.308 63.158 0.00 0.00 0.00 4.37
582 658 1.004230 TGGGGTGGGAGTATGGGAG 59.996 63.158 0.00 0.00 0.00 4.30
583 659 1.004361 GGGGTGGGAGTATGGGAGT 59.996 63.158 0.00 0.00 0.00 3.85
584 660 1.345715 GGGGTGGGAGTATGGGAGTG 61.346 65.000 0.00 0.00 0.00 3.51
585 661 0.620700 GGGTGGGAGTATGGGAGTGT 60.621 60.000 0.00 0.00 0.00 3.55
586 662 1.286248 GGTGGGAGTATGGGAGTGTT 58.714 55.000 0.00 0.00 0.00 3.32
587 663 1.065418 GGTGGGAGTATGGGAGTGTTG 60.065 57.143 0.00 0.00 0.00 3.33
588 664 1.906574 GTGGGAGTATGGGAGTGTTGA 59.093 52.381 0.00 0.00 0.00 3.18
589 665 1.906574 TGGGAGTATGGGAGTGTTGAC 59.093 52.381 0.00 0.00 0.00 3.18
590 666 2.188817 GGGAGTATGGGAGTGTTGACT 58.811 52.381 0.00 0.00 33.98 3.41
591 667 2.572104 GGGAGTATGGGAGTGTTGACTT 59.428 50.000 0.00 0.00 30.16 3.01
592 668 3.773119 GGGAGTATGGGAGTGTTGACTTA 59.227 47.826 0.00 0.00 30.16 2.24
593 669 4.141914 GGGAGTATGGGAGTGTTGACTTAG 60.142 50.000 0.00 0.00 30.16 2.18
594 670 4.710375 GGAGTATGGGAGTGTTGACTTAGA 59.290 45.833 0.00 0.00 30.16 2.10
595 671 5.163499 GGAGTATGGGAGTGTTGACTTAGAG 60.163 48.000 0.00 0.00 30.16 2.43
596 672 4.712337 AGTATGGGAGTGTTGACTTAGAGG 59.288 45.833 0.00 0.00 30.16 3.69
597 673 1.623811 TGGGAGTGTTGACTTAGAGGC 59.376 52.381 0.00 0.00 30.16 4.70
598 674 1.903183 GGGAGTGTTGACTTAGAGGCT 59.097 52.381 0.00 0.00 30.16 4.58
599 675 2.093921 GGGAGTGTTGACTTAGAGGCTC 60.094 54.545 6.34 6.34 30.16 4.70
600 676 2.563179 GGAGTGTTGACTTAGAGGCTCA 59.437 50.000 18.26 0.00 30.16 4.26
601 677 3.580731 GAGTGTTGACTTAGAGGCTCAC 58.419 50.000 18.26 4.58 32.25 3.51
602 678 2.029828 AGTGTTGACTTAGAGGCTCACG 60.030 50.000 18.26 6.72 35.31 4.35
603 679 1.272490 TGTTGACTTAGAGGCTCACGG 59.728 52.381 18.26 8.08 0.00 4.94
604 680 1.272769 GTTGACTTAGAGGCTCACGGT 59.727 52.381 18.26 11.31 0.00 4.83
605 681 1.629043 TGACTTAGAGGCTCACGGTT 58.371 50.000 18.26 0.00 0.00 4.44
606 682 1.968493 TGACTTAGAGGCTCACGGTTT 59.032 47.619 18.26 0.00 0.00 3.27
607 683 2.029290 TGACTTAGAGGCTCACGGTTTC 60.029 50.000 18.26 5.68 0.00 2.78
608 684 1.275573 ACTTAGAGGCTCACGGTTTCC 59.724 52.381 18.26 0.00 0.00 3.13
734 877 4.555709 GCGTGGTGGTGGTGGTGA 62.556 66.667 0.00 0.00 0.00 4.02
735 878 2.429930 CGTGGTGGTGGTGGTGAT 59.570 61.111 0.00 0.00 0.00 3.06
737 880 1.603455 GTGGTGGTGGTGGTGATGG 60.603 63.158 0.00 0.00 0.00 3.51
738 881 2.676471 GGTGGTGGTGGTGATGGC 60.676 66.667 0.00 0.00 0.00 4.40
739 882 2.436109 GTGGTGGTGGTGATGGCT 59.564 61.111 0.00 0.00 0.00 4.75
740 883 1.973281 GTGGTGGTGGTGATGGCTG 60.973 63.158 0.00 0.00 0.00 4.85
741 884 2.361610 GGTGGTGGTGATGGCTGG 60.362 66.667 0.00 0.00 0.00 4.85
742 885 2.361610 GTGGTGGTGATGGCTGGG 60.362 66.667 0.00 0.00 0.00 4.45
743 886 2.858476 TGGTGGTGATGGCTGGGT 60.858 61.111 0.00 0.00 0.00 4.51
744 887 1.540118 TGGTGGTGATGGCTGGGTA 60.540 57.895 0.00 0.00 0.00 3.69
745 888 1.136961 TGGTGGTGATGGCTGGGTAA 61.137 55.000 0.00 0.00 0.00 2.85
746 889 0.039035 GGTGGTGATGGCTGGGTAAA 59.961 55.000 0.00 0.00 0.00 2.01
758 902 0.759959 TGGGTAAAGGCAACGAGTGA 59.240 50.000 0.00 0.00 46.39 3.41
768 912 7.865706 AAAGGCAACGAGTGAATAAATATCT 57.134 32.000 0.00 0.00 46.39 1.98
770 914 9.561069 AAAGGCAACGAGTGAATAAATATCTAT 57.439 29.630 0.00 0.00 46.39 1.98
790 4303 2.802719 TCCCAGGCTTAATTTTTCGCT 58.197 42.857 0.00 0.00 0.00 4.93
920 4435 2.310538 GCCCATCAGTCCCCATTTTAG 58.689 52.381 0.00 0.00 0.00 1.85
921 4436 2.358195 GCCCATCAGTCCCCATTTTAGT 60.358 50.000 0.00 0.00 0.00 2.24
922 4437 3.881713 GCCCATCAGTCCCCATTTTAGTT 60.882 47.826 0.00 0.00 0.00 2.24
923 4438 3.701040 CCCATCAGTCCCCATTTTAGTTG 59.299 47.826 0.00 0.00 0.00 3.16
924 4439 4.569653 CCCATCAGTCCCCATTTTAGTTGA 60.570 45.833 0.00 0.00 0.00 3.18
925 4440 4.641989 CCATCAGTCCCCATTTTAGTTGAG 59.358 45.833 0.00 0.00 0.00 3.02
926 4441 4.993705 TCAGTCCCCATTTTAGTTGAGT 57.006 40.909 0.00 0.00 0.00 3.41
1224 4784 4.016706 AAGCCACCGCCGCTACTT 62.017 61.111 0.00 0.00 34.84 2.24
1274 4834 2.439156 GCGGCCCATCTTCAAGCT 60.439 61.111 0.00 0.00 0.00 3.74
1769 5682 6.095377 GCATCCTCGAGTTTGATTTTGAAAT 58.905 36.000 12.31 0.00 0.00 2.17
1817 5745 2.029728 CAGCAGACGTTAATGTAGCAGC 59.970 50.000 20.50 13.29 0.00 5.25
1904 5848 2.297597 AGCCAGATTATCAGAGCGGTAC 59.702 50.000 0.00 0.00 0.00 3.34
2138 6177 2.346803 TCTTATTGAACACCAGAGCGC 58.653 47.619 0.00 0.00 0.00 5.92
2151 6190 2.351641 CCAGAGCGCTTGCATTTTTACA 60.352 45.455 13.26 0.00 42.66 2.41
2214 6267 1.561643 CCTTGTCCCTGTCTGCTCTA 58.438 55.000 0.00 0.00 0.00 2.43
2423 6601 9.698309 ATCTTTACTATCATACATGGAGAAACG 57.302 33.333 0.00 0.00 0.00 3.60
2665 6877 7.095017 GCCTAGCAGTAGATATGGTTTCATTTC 60.095 40.741 0.00 0.00 34.96 2.17
2685 6897 1.408266 CCCCCATTCCTACCTTTGTCG 60.408 57.143 0.00 0.00 0.00 4.35
2686 6898 1.280998 CCCCATTCCTACCTTTGTCGT 59.719 52.381 0.00 0.00 0.00 4.34
2687 6899 2.629051 CCCATTCCTACCTTTGTCGTC 58.371 52.381 0.00 0.00 0.00 4.20
2775 6995 0.821711 TTTTGCTTGTAGGCAGCGGT 60.822 50.000 0.00 0.00 43.39 5.68
2858 7084 7.773224 AGGTATGCTAATGTGCTATGTTTGTTA 59.227 33.333 0.00 0.00 0.00 2.41
2893 7120 9.787532 ATGTGGATTTATTGTTTTTCTACATCG 57.212 29.630 0.00 0.00 34.64 3.84
3019 7266 7.088905 ACAAGTGAATGATGCTTCTGATTTTC 58.911 34.615 0.88 0.00 0.00 2.29
3135 7760 6.206395 TCATTTGTTTCTTGAAGTGAAGCA 57.794 33.333 0.00 0.00 33.92 3.91
3188 7815 0.734889 CCTTATTCCAGGCTTGCACG 59.265 55.000 0.00 0.00 0.00 5.34
3221 7848 3.551890 CAGATGCAATGCAAGCTGATTTC 59.448 43.478 26.61 12.81 43.01 2.17
3347 7978 8.693120 ATCTAAGCTGCATTAGTACTGTACTA 57.307 34.615 20.74 20.74 40.14 1.82
3523 8164 5.063204 TGTTTCAGTTGAGTAATGAGTGGG 58.937 41.667 0.00 0.00 0.00 4.61
3603 8247 8.333186 GGCTTTGAAAATGATTAGAATTGATGC 58.667 33.333 0.00 0.00 0.00 3.91
3638 8283 3.129109 AGCGTGATGAGCATGAATACTG 58.871 45.455 0.00 0.00 35.44 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.829003 CGGCTCCGACAGGCTAGA 60.829 66.667 1.35 0.00 45.92 2.43
22 23 2.969238 CCGACATGATGAGCGGGC 60.969 66.667 18.59 0.00 36.06 6.13
64 65 0.463654 GGATACCGTGCAGGCAATCA 60.464 55.000 16.25 0.00 46.52 2.57
334 410 4.514577 CATCGACTTCGCCGCCCT 62.515 66.667 0.00 0.00 39.60 5.19
398 474 1.373497 CTCAAACTCGCCGAGCTGT 60.373 57.895 15.20 0.00 32.04 4.40
557 633 2.758852 TACTCCCACCCCACTCCACC 62.759 65.000 0.00 0.00 0.00 4.61
558 634 0.620700 ATACTCCCACCCCACTCCAC 60.621 60.000 0.00 0.00 0.00 4.02
559 635 0.620410 CATACTCCCACCCCACTCCA 60.620 60.000 0.00 0.00 0.00 3.86
560 636 1.345715 CCATACTCCCACCCCACTCC 61.346 65.000 0.00 0.00 0.00 3.85
561 637 1.345715 CCCATACTCCCACCCCACTC 61.346 65.000 0.00 0.00 0.00 3.51
562 638 1.307866 CCCATACTCCCACCCCACT 60.308 63.158 0.00 0.00 0.00 4.00
563 639 1.307517 TCCCATACTCCCACCCCAC 60.308 63.158 0.00 0.00 0.00 4.61
564 640 1.004230 CTCCCATACTCCCACCCCA 59.996 63.158 0.00 0.00 0.00 4.96
565 641 1.004361 ACTCCCATACTCCCACCCC 59.996 63.158 0.00 0.00 0.00 4.95
566 642 0.620700 ACACTCCCATACTCCCACCC 60.621 60.000 0.00 0.00 0.00 4.61
567 643 1.065418 CAACACTCCCATACTCCCACC 60.065 57.143 0.00 0.00 0.00 4.61
568 644 1.906574 TCAACACTCCCATACTCCCAC 59.093 52.381 0.00 0.00 0.00 4.61
569 645 1.906574 GTCAACACTCCCATACTCCCA 59.093 52.381 0.00 0.00 0.00 4.37
570 646 2.188817 AGTCAACACTCCCATACTCCC 58.811 52.381 0.00 0.00 0.00 4.30
571 647 3.983044 AAGTCAACACTCCCATACTCC 57.017 47.619 0.00 0.00 29.93 3.85
572 648 5.163499 CCTCTAAGTCAACACTCCCATACTC 60.163 48.000 0.00 0.00 29.93 2.59
573 649 4.712337 CCTCTAAGTCAACACTCCCATACT 59.288 45.833 0.00 0.00 29.93 2.12
574 650 4.680975 GCCTCTAAGTCAACACTCCCATAC 60.681 50.000 0.00 0.00 29.93 2.39
575 651 3.451178 GCCTCTAAGTCAACACTCCCATA 59.549 47.826 0.00 0.00 29.93 2.74
576 652 2.237392 GCCTCTAAGTCAACACTCCCAT 59.763 50.000 0.00 0.00 29.93 4.00
577 653 1.623811 GCCTCTAAGTCAACACTCCCA 59.376 52.381 0.00 0.00 29.93 4.37
578 654 1.903183 AGCCTCTAAGTCAACACTCCC 59.097 52.381 0.00 0.00 29.93 4.30
579 655 2.563179 TGAGCCTCTAAGTCAACACTCC 59.437 50.000 0.00 0.00 29.93 3.85
580 656 3.580731 GTGAGCCTCTAAGTCAACACTC 58.419 50.000 0.00 0.00 29.93 3.51
581 657 2.029828 CGTGAGCCTCTAAGTCAACACT 60.030 50.000 0.00 0.00 0.00 3.55
582 658 2.329379 CGTGAGCCTCTAAGTCAACAC 58.671 52.381 0.00 0.00 0.00 3.32
583 659 1.272490 CCGTGAGCCTCTAAGTCAACA 59.728 52.381 0.00 0.00 0.00 3.33
584 660 1.272769 ACCGTGAGCCTCTAAGTCAAC 59.727 52.381 0.00 0.00 0.00 3.18
585 661 1.629043 ACCGTGAGCCTCTAAGTCAA 58.371 50.000 0.00 0.00 0.00 3.18
586 662 1.629043 AACCGTGAGCCTCTAAGTCA 58.371 50.000 0.00 0.00 0.00 3.41
587 663 2.608268 GAAACCGTGAGCCTCTAAGTC 58.392 52.381 0.00 0.00 0.00 3.01
588 664 1.275573 GGAAACCGTGAGCCTCTAAGT 59.724 52.381 0.00 0.00 0.00 2.24
589 665 1.736032 CGGAAACCGTGAGCCTCTAAG 60.736 57.143 1.80 0.00 42.73 2.18
590 666 0.245539 CGGAAACCGTGAGCCTCTAA 59.754 55.000 1.80 0.00 42.73 2.10
591 667 1.888018 CGGAAACCGTGAGCCTCTA 59.112 57.895 1.80 0.00 42.73 2.43
592 668 2.657237 CGGAAACCGTGAGCCTCT 59.343 61.111 1.80 0.00 42.73 3.69
732 875 0.407528 TTGCCTTTACCCAGCCATCA 59.592 50.000 0.00 0.00 0.00 3.07
733 876 0.817654 GTTGCCTTTACCCAGCCATC 59.182 55.000 0.00 0.00 0.00 3.51
734 877 0.965363 CGTTGCCTTTACCCAGCCAT 60.965 55.000 0.00 0.00 0.00 4.40
735 878 1.602323 CGTTGCCTTTACCCAGCCA 60.602 57.895 0.00 0.00 0.00 4.75
737 880 0.605589 ACTCGTTGCCTTTACCCAGC 60.606 55.000 0.00 0.00 0.00 4.85
738 881 1.156736 CACTCGTTGCCTTTACCCAG 58.843 55.000 0.00 0.00 0.00 4.45
739 882 0.759959 TCACTCGTTGCCTTTACCCA 59.240 50.000 0.00 0.00 0.00 4.51
740 883 1.886886 TTCACTCGTTGCCTTTACCC 58.113 50.000 0.00 0.00 0.00 3.69
741 884 5.616488 TTTATTCACTCGTTGCCTTTACC 57.384 39.130 0.00 0.00 0.00 2.85
742 885 8.827677 AGATATTTATTCACTCGTTGCCTTTAC 58.172 33.333 0.00 0.00 0.00 2.01
743 886 8.958119 AGATATTTATTCACTCGTTGCCTTTA 57.042 30.769 0.00 0.00 0.00 1.85
744 887 7.865706 AGATATTTATTCACTCGTTGCCTTT 57.134 32.000 0.00 0.00 0.00 3.11
745 888 9.209175 GATAGATATTTATTCACTCGTTGCCTT 57.791 33.333 0.00 0.00 0.00 4.35
746 889 7.819900 GGATAGATATTTATTCACTCGTTGCCT 59.180 37.037 0.00 0.00 0.00 4.75
768 912 4.338118 CAGCGAAAAATTAAGCCTGGGATA 59.662 41.667 0.00 0.00 0.00 2.59
770 914 2.491693 CAGCGAAAAATTAAGCCTGGGA 59.508 45.455 0.00 0.00 0.00 4.37
824 4337 0.734253 CTCCAGCCGTTGAGTCTTCG 60.734 60.000 0.00 0.00 0.00 3.79
829 4344 1.137872 GATCATCTCCAGCCGTTGAGT 59.862 52.381 0.00 0.00 0.00 3.41
920 4435 0.549413 AAGGGGTAGGGGGACTCAAC 60.549 60.000 0.00 0.00 0.00 3.18
921 4436 0.253020 GAAGGGGTAGGGGGACTCAA 60.253 60.000 0.00 0.00 0.00 3.02
922 4437 1.394963 GAAGGGGTAGGGGGACTCA 59.605 63.158 0.00 0.00 0.00 3.41
923 4438 0.981801 GTGAAGGGGTAGGGGGACTC 60.982 65.000 0.00 0.00 0.00 3.36
924 4439 1.082392 GTGAAGGGGTAGGGGGACT 59.918 63.158 0.00 0.00 0.00 3.85
925 4440 0.981801 GAGTGAAGGGGTAGGGGGAC 60.982 65.000 0.00 0.00 0.00 4.46
926 4441 1.394963 GAGTGAAGGGGTAGGGGGA 59.605 63.158 0.00 0.00 0.00 4.81
1224 4784 0.895530 ATTCCTCGTCGAAGAAGCCA 59.104 50.000 11.64 0.00 39.69 4.75
1769 5682 0.615331 GATCACCACAAGGCTCTGGA 59.385 55.000 16.15 0.00 39.06 3.86
1817 5745 1.204941 CGAGAAAGGACCAGTGGTAGG 59.795 57.143 16.72 0.00 35.25 3.18
1904 5848 7.008941 AGATTTTCTCTCCCATAATTGGATGG 58.991 38.462 0.76 0.76 46.92 3.51
2138 6177 9.736023 GATAATAGGTCCTTGTAAAAATGCAAG 57.264 33.333 0.00 0.41 41.08 4.01
2151 6190 7.613551 ATTTCTGTACGGATAATAGGTCCTT 57.386 36.000 4.94 0.00 33.46 3.36
2214 6267 8.947115 GTTAGAAAGAACATGCTAAATACACCT 58.053 33.333 0.00 0.00 0.00 4.00
2423 6601 4.305989 TCAGGTTCAATGAACAAGCAAC 57.694 40.909 25.14 8.74 43.54 4.17
2665 6877 1.408266 CGACAAAGGTAGGAATGGGGG 60.408 57.143 0.00 0.00 0.00 5.40
2685 6897 5.710567 AGAAGGCAAAACTACCCTTTATGAC 59.289 40.000 0.00 0.00 38.99 3.06
2686 6898 5.887754 AGAAGGCAAAACTACCCTTTATGA 58.112 37.500 0.00 0.00 38.99 2.15
2687 6899 5.710099 TGAGAAGGCAAAACTACCCTTTATG 59.290 40.000 0.00 0.00 38.99 1.90
2775 6995 0.034756 CACCATCTCGACCACCAACA 59.965 55.000 0.00 0.00 0.00 3.33
2858 7084 9.612066 AAAACAATAAATCCACATCACTTGTTT 57.388 25.926 0.00 0.00 43.50 2.83
2934 7164 8.768397 TGATTACACCCAGTTCAGTTCTAATAT 58.232 33.333 0.00 0.00 0.00 1.28
2942 7172 5.186198 GCTAATGATTACACCCAGTTCAGT 58.814 41.667 0.00 0.00 0.00 3.41
2952 7182 7.042187 CCAACTGATCTCTGCTAATGATTACAC 60.042 40.741 0.00 0.00 0.00 2.90
3040 7288 5.874810 ACACACATTCATCTACGCTGTAATT 59.125 36.000 0.00 0.00 0.00 1.40
3041 7289 5.419542 ACACACATTCATCTACGCTGTAAT 58.580 37.500 0.00 0.00 0.00 1.89
3042 7290 4.816392 ACACACATTCATCTACGCTGTAA 58.184 39.130 0.00 0.00 0.00 2.41
3135 7760 6.610075 AGTTGCAGGGAAAATATGACAAAT 57.390 33.333 0.00 0.00 0.00 2.32
3165 7790 1.339291 GCAAGCCTGGAATAAGGATGC 59.661 52.381 0.00 5.92 41.48 3.91
3188 7815 4.110482 GCATTGCATCTGAAATCTCCAAC 58.890 43.478 3.15 0.00 0.00 3.77
3270 7901 5.598416 ATCACCGAGATGTCACTAATTCA 57.402 39.130 0.00 0.00 35.06 2.57
3357 7988 6.511767 CGACACTACAAAGCAAAGAACAGAAT 60.512 38.462 0.00 0.00 0.00 2.40
3362 7993 4.506654 TCTCGACACTACAAAGCAAAGAAC 59.493 41.667 0.00 0.00 0.00 3.01
3365 7996 4.606232 CGTTCTCGACACTACAAAGCAAAG 60.606 45.833 0.00 0.00 39.71 2.77
3557 8198 8.878769 CAAAGCCAAAACTAACAAACAAGTAAT 58.121 29.630 0.00 0.00 0.00 1.89
3603 8247 2.317609 ACGCTTGCGGTTACAGCAG 61.318 57.895 19.19 6.45 46.01 4.24


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

AutoCloner maintained by Alex Coulton.