Multiple sequence alignment - TraesCS3D01G497400

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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 TraesCS3D01G497400 chr3D 100.000 3819 0 0 1 3819 588693910 588697728 0.000000e+00 7053
1 TraesCS3D01G497400 chr3D 97.835 3556 73 4 1 3555 10935662 10932110 0.000000e+00 6137
2 TraesCS3D01G497400 chr3D 96.896 451 10 4 3105 3555 564469366 564468920 0.000000e+00 752
3 TraesCS3D01G497400 chr3D 96.674 451 13 2 3105 3555 436319840 436320288 0.000000e+00 749
4 TraesCS3D01G497400 chr3D 88.933 506 33 9 1 486 45395287 45395789 1.520000e-168 603
5 TraesCS3D01G497400 chr3D 98.611 144 2 0 3676 3819 10932114 10931971 4.900000e-64 255
6 TraesCS3D01G497400 chr3D 98.438 128 2 0 3552 3679 160615986 160615859 3.840000e-55 226
7 TraesCS3D01G497400 chr3D 94.928 138 6 1 3545 3682 254739731 254739867 8.310000e-52 215
8 TraesCS3D01G497400 chr6D 97.272 3556 80 8 1 3555 372615966 372612427 0.000000e+00 6013
9 TraesCS3D01G497400 chr6D 95.956 1088 40 4 784 1869 163424609 163425694 0.000000e+00 1762
10 TraesCS3D01G497400 chr6D 97.222 144 4 0 3676 3819 372612431 372612288 1.060000e-60 244
11 TraesCS3D01G497400 chr6D 98.425 127 2 0 3552 3678 109243645 109243519 1.380000e-54 224
12 TraesCS3D01G497400 chr5A 96.455 3357 102 10 1 3350 155589440 155592786 0.000000e+00 5524
13 TraesCS3D01G497400 chr5A 95.023 1286 59 5 1 1284 497932684 497933966 0.000000e+00 2015
14 TraesCS3D01G497400 chr5A 96.063 127 5 0 3552 3678 557575173 557575299 1.390000e-49 207
15 TraesCS3D01G497400 chr5D 96.916 1978 57 4 1579 3555 556579374 556577400 0.000000e+00 3312
16 TraesCS3D01G497400 chr5D 91.722 302 13 6 484 784 287878938 287878648 3.550000e-110 409
17 TraesCS3D01G497400 chr5D 97.917 144 3 0 3676 3819 556577404 556577261 2.280000e-62 250
18 TraesCS3D01G497400 chr2D 96.915 1977 58 2 1579 3555 586830299 586832272 0.000000e+00 3310
19 TraesCS3D01G497400 chr2D 97.222 144 4 0 3676 3819 586832268 586832411 1.060000e-60 244
20 TraesCS3D01G497400 chr1B 95.799 2047 75 5 1516 3555 137870254 137872296 0.000000e+00 3293
21 TraesCS3D01G497400 chr7B 95.894 1242 48 1 1869 3110 97120866 97119628 0.000000e+00 2008
22 TraesCS3D01G497400 chr7B 94.767 1242 53 4 1869 3110 89870745 89869516 0.000000e+00 1923
23 TraesCS3D01G497400 chr7B 97.222 144 4 0 3676 3819 97117901 97117758 1.060000e-60 244
24 TraesCS3D01G497400 chr1A 95.516 1249 55 1 2307 3555 379647386 379648633 0.000000e+00 1995
25 TraesCS3D01G497400 chr1A 97.222 144 4 0 3676 3819 379648629 379648772 1.060000e-60 244
26 TraesCS3D01G497400 chr4D 96.504 1087 34 4 784 1869 500937159 500936076 0.000000e+00 1794
27 TraesCS3D01G497400 chr4D 96.412 1087 35 4 784 1869 500975893 500974810 0.000000e+00 1788
28 TraesCS3D01G497400 chr4D 96.136 1087 35 5 784 1869 500899303 500898223 0.000000e+00 1768
29 TraesCS3D01G497400 chr4D 91.722 302 13 5 484 784 457303348 457303058 3.550000e-110 409
30 TraesCS3D01G497400 chr4D 97.600 125 3 0 3555 3679 108906247 108906371 8.310000e-52 215
31 TraesCS3D01G497400 chr4D 94.815 135 7 0 3544 3678 337135963 337136097 1.070000e-50 211
32 TraesCS3D01G497400 chr6B 95.488 1086 46 3 784 1869 628512109 628513191 0.000000e+00 1731
33 TraesCS3D01G497400 chr6B 95.681 301 13 0 484 784 628511741 628512041 5.740000e-133 484
34 TraesCS3D01G497400 chr6B 95.652 299 11 2 488 785 552851222 552850925 2.670000e-131 479
35 TraesCS3D01G497400 chr6B 91.111 135 11 1 2977 3110 128212033 128212167 8.430000e-42 182
36 TraesCS3D01G497400 chr3A 95.492 1087 44 5 784 1869 401133458 401134540 0.000000e+00 1731
37 TraesCS3D01G497400 chr3A 89.189 185 18 2 12 196 57158627 57158809 2.970000e-56 230
38 TraesCS3D01G497400 chr3A 83.077 195 28 4 1 191 64047664 64047857 5.070000e-39 172
39 TraesCS3D01G497400 chr5B 96.078 459 18 0 1516 1974 652146254 652145796 0.000000e+00 749
40 TraesCS3D01G497400 chr5B 95.861 459 19 0 1516 1974 651941021 651940563 0.000000e+00 743
41 TraesCS3D01G497400 chr5B 97.917 144 3 0 3676 3819 528385938 528385795 2.280000e-62 250
42 TraesCS3D01G497400 chr2B 95.050 303 14 1 484 785 553516217 553515915 3.450000e-130 475
43 TraesCS3D01G497400 chr2B 93.627 204 13 0 1882 2085 43958051 43958254 4.790000e-79 305
44 TraesCS3D01G497400 chr2B 97.222 144 4 0 3676 3819 263981507 263981650 1.060000e-60 244
45 TraesCS3D01G497400 chr3B 97.902 143 3 0 3676 3818 686222321 686222463 8.190000e-62 248
46 TraesCS3D01G497400 chr3B 88.060 201 22 2 1 201 70965565 70965763 1.770000e-58 237
47 TraesCS3D01G497400 chr3B 83.085 201 28 5 1 196 82060662 82060861 1.090000e-40 178
48 TraesCS3D01G497400 chr1D 97.692 130 3 0 3552 3681 465522002 465522131 1.380000e-54 224
49 TraesCS3D01G497400 chr1D 96.875 128 4 0 3552 3679 270226763 270226890 8.310000e-52 215
50 TraesCS3D01G497400 chr7A 93.333 135 9 0 3548 3682 680419117 680418983 2.330000e-47 200


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 TraesCS3D01G497400 chr3D 588693910 588697728 3818 False 7053.0 7053 100.0000 1 3819 1 chr3D.!!$F4 3818
1 TraesCS3D01G497400 chr3D 10931971 10935662 3691 True 3196.0 6137 98.2230 1 3819 2 chr3D.!!$R3 3818
2 TraesCS3D01G497400 chr3D 45395287 45395789 502 False 603.0 603 88.9330 1 486 1 chr3D.!!$F1 485
3 TraesCS3D01G497400 chr6D 372612288 372615966 3678 True 3128.5 6013 97.2470 1 3819 2 chr6D.!!$R2 3818
4 TraesCS3D01G497400 chr6D 163424609 163425694 1085 False 1762.0 1762 95.9560 784 1869 1 chr6D.!!$F1 1085
5 TraesCS3D01G497400 chr5A 155589440 155592786 3346 False 5524.0 5524 96.4550 1 3350 1 chr5A.!!$F1 3349
6 TraesCS3D01G497400 chr5A 497932684 497933966 1282 False 2015.0 2015 95.0230 1 1284 1 chr5A.!!$F2 1283
7 TraesCS3D01G497400 chr5D 556577261 556579374 2113 True 1781.0 3312 97.4165 1579 3819 2 chr5D.!!$R2 2240
8 TraesCS3D01G497400 chr2D 586830299 586832411 2112 False 1777.0 3310 97.0685 1579 3819 2 chr2D.!!$F1 2240
9 TraesCS3D01G497400 chr1B 137870254 137872296 2042 False 3293.0 3293 95.7990 1516 3555 1 chr1B.!!$F1 2039
10 TraesCS3D01G497400 chr7B 89869516 89870745 1229 True 1923.0 1923 94.7670 1869 3110 1 chr7B.!!$R1 1241
11 TraesCS3D01G497400 chr7B 97117758 97120866 3108 True 1126.0 2008 96.5580 1869 3819 2 chr7B.!!$R2 1950
12 TraesCS3D01G497400 chr1A 379647386 379648772 1386 False 1119.5 1995 96.3690 2307 3819 2 chr1A.!!$F1 1512
13 TraesCS3D01G497400 chr4D 500936076 500937159 1083 True 1794.0 1794 96.5040 784 1869 1 chr4D.!!$R3 1085
14 TraesCS3D01G497400 chr4D 500974810 500975893 1083 True 1788.0 1788 96.4120 784 1869 1 chr4D.!!$R4 1085
15 TraesCS3D01G497400 chr4D 500898223 500899303 1080 True 1768.0 1768 96.1360 784 1869 1 chr4D.!!$R2 1085
16 TraesCS3D01G497400 chr6B 628511741 628513191 1450 False 1107.5 1731 95.5845 484 1869 2 chr6B.!!$F2 1385
17 TraesCS3D01G497400 chr3A 401133458 401134540 1082 False 1731.0 1731 95.4920 784 1869 1 chr3A.!!$F3 1085

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
527 548 1.663695 CTGTCAAAACTCGGTGGTGT 58.336 50.0 0.0 0.0 0.0 4.16 F
1885 1990 1.509644 CGCACACAGGTCAACATGCT 61.510 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2058 1.346395 TCACGGCCACTGATTACTTGT 59.654 47.619 2.24 0.0 0.0 3.16 R
3667 5064 0.175989 GGCTTCAAGTACTCCCTCCG 59.824 60.000 0.00 0.0 0.0 4.63 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 3.774959 ATGCCGCGTCGAGTCCATC 62.775 63.158 4.92 0.00 0.00 3.51
332 350 4.971924 AGTGGTTCCTAGCTGAATCCTTAT 59.028 41.667 0.00 0.00 0.00 1.73
411 431 6.491062 AGTCCATCAAACATGATTTGAACTCA 59.509 34.615 20.00 8.23 41.16 3.41
527 548 1.663695 CTGTCAAAACTCGGTGGTGT 58.336 50.000 0.00 0.00 0.00 4.16
695 716 4.640201 GCCATTTAGTACAGAAGGATGCAA 59.360 41.667 0.00 0.00 0.00 4.08
1123 1213 2.686106 GGGAGGTCGGCCCTTGTA 60.686 66.667 0.08 0.00 46.51 2.41
1297 1388 6.444633 TGTAGAGTTGTAGCTTGACACTTAC 58.555 40.000 0.00 0.00 0.00 2.34
1494 1585 4.618920 ATCGAGTACAACAAACCTCCTT 57.381 40.909 0.00 0.00 0.00 3.36
1496 1587 5.534207 TCGAGTACAACAAACCTCCTTTA 57.466 39.130 0.00 0.00 0.00 1.85
1885 1990 1.509644 CGCACACAGGTCAACATGCT 61.510 55.000 0.00 0.00 0.00 3.79
1898 2003 7.228108 CAGGTCAACATGCTCTGTTTATATGAT 59.772 37.037 0.00 0.00 45.98 2.45
1953 2058 3.484557 GATTAAAATCTCCGCGCAACGAA 60.485 43.478 8.75 0.00 36.82 3.85
2031 2136 5.899120 AGAAGTAATACTTGACTGCTCGA 57.101 39.130 10.76 0.00 38.80 4.04
2338 2443 2.638480 TCCTGTTGCTTGTTGCTAGT 57.362 45.000 0.00 0.00 43.37 2.57
2361 2466 5.560722 TGTAGGATCTGACTTTTGGTTGA 57.439 39.130 0.00 0.00 0.00 3.18
2892 3000 2.909006 TGCTTCCTCCTTGAGTTCAGAT 59.091 45.455 0.00 0.00 0.00 2.90
3036 3145 3.074412 GTTTTGCTACTGCTCCTGCTAA 58.926 45.455 0.00 0.00 40.48 3.09
3465 4862 4.382254 CCTTGGCATGCATATGTTTGTTCT 60.382 41.667 21.36 0.00 36.65 3.01
3488 4885 5.042593 TGTTTGAACTTTGCATGACATGAC 58.957 37.500 19.76 10.72 0.00 3.06
3558 4955 9.824216 TTGATATATACTTAGCTTGTACTCCCT 57.176 33.333 0.00 0.00 0.00 4.20
3559 4956 9.463902 TGATATATACTTAGCTTGTACTCCCTC 57.536 37.037 0.00 0.00 0.00 4.30
3560 4957 8.826293 ATATATACTTAGCTTGTACTCCCTCC 57.174 38.462 0.00 0.00 0.00 4.30
3561 4958 2.100989 ACTTAGCTTGTACTCCCTCCG 58.899 52.381 0.00 0.00 0.00 4.63
3562 4959 2.100989 CTTAGCTTGTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
3563 4960 2.226962 TAGCTTGTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
3564 4961 0.896226 AGCTTGTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
3565 4962 0.108281 GCTTGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
3566 4963 0.172803 CTTGTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
3567 4964 0.251297 TTGTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
3568 4965 0.679002 TGTACTCCCTCCGTTCCGAG 60.679 60.000 0.00 0.00 0.00 4.63
3569 4966 0.679321 GTACTCCCTCCGTTCCGAGT 60.679 60.000 0.00 0.00 38.97 4.18
3570 4967 0.038744 TACTCCCTCCGTTCCGAGTT 59.961 55.000 0.00 0.00 36.91 3.01
3571 4968 0.038744 ACTCCCTCCGTTCCGAGTTA 59.961 55.000 0.00 0.00 31.58 2.24
3572 4969 0.455005 CTCCCTCCGTTCCGAGTTAC 59.545 60.000 0.00 0.00 0.00 2.50
3573 4970 0.038744 TCCCTCCGTTCCGAGTTACT 59.961 55.000 0.00 0.00 0.00 2.24
3574 4971 0.893447 CCCTCCGTTCCGAGTTACTT 59.107 55.000 0.00 0.00 0.00 2.24
3575 4972 1.403780 CCCTCCGTTCCGAGTTACTTG 60.404 57.143 0.00 0.00 0.00 3.16
3576 4973 1.271656 CCTCCGTTCCGAGTTACTTGT 59.728 52.381 0.00 0.00 0.00 3.16
3577 4974 2.593257 CTCCGTTCCGAGTTACTTGTC 58.407 52.381 0.00 0.00 0.00 3.18
3578 4975 2.228343 CTCCGTTCCGAGTTACTTGTCT 59.772 50.000 0.00 0.00 0.00 3.41
3579 4976 2.624838 TCCGTTCCGAGTTACTTGTCTT 59.375 45.455 0.00 0.00 0.00 3.01
3580 4977 2.729882 CCGTTCCGAGTTACTTGTCTTG 59.270 50.000 0.00 0.00 0.00 3.02
3581 4978 2.729882 CGTTCCGAGTTACTTGTCTTGG 59.270 50.000 0.00 0.00 36.76 3.61
3582 4979 3.551454 CGTTCCGAGTTACTTGTCTTGGA 60.551 47.826 0.00 0.00 41.05 3.53
3583 4980 4.566987 GTTCCGAGTTACTTGTCTTGGAT 58.433 43.478 0.00 0.00 41.95 3.41
3584 4981 4.884668 TCCGAGTTACTTGTCTTGGATT 57.115 40.909 0.00 0.00 38.78 3.01
3585 4982 5.223449 TCCGAGTTACTTGTCTTGGATTT 57.777 39.130 0.00 0.00 38.78 2.17
3586 4983 6.349243 TCCGAGTTACTTGTCTTGGATTTA 57.651 37.500 0.00 0.00 38.78 1.40
3587 4984 6.942976 TCCGAGTTACTTGTCTTGGATTTAT 58.057 36.000 0.00 0.00 38.78 1.40
3588 4985 7.039882 TCCGAGTTACTTGTCTTGGATTTATC 58.960 38.462 0.00 0.00 38.78 1.75
3589 4986 7.042335 CCGAGTTACTTGTCTTGGATTTATCT 58.958 38.462 0.00 0.00 37.40 1.98
3590 4987 8.195436 CCGAGTTACTTGTCTTGGATTTATCTA 58.805 37.037 0.00 0.00 37.40 1.98
3591 4988 9.239002 CGAGTTACTTGTCTTGGATTTATCTAG 57.761 37.037 0.00 0.00 0.00 2.43
3600 4997 8.523658 TGTCTTGGATTTATCTAGATACATCCG 58.476 37.037 33.19 25.69 46.32 4.18
3601 4998 8.524487 GTCTTGGATTTATCTAGATACATCCGT 58.476 37.037 33.19 10.18 46.32 4.69
3602 4999 9.749340 TCTTGGATTTATCTAGATACATCCGTA 57.251 33.333 33.19 26.65 46.32 4.02
3620 5017 9.698309 ACATCCGTATCTAGATTCATTTTAGTG 57.302 33.333 11.25 2.32 0.00 2.74
3621 5018 8.651588 CATCCGTATCTAGATTCATTTTAGTGC 58.348 37.037 11.25 0.00 0.00 4.40
3622 5019 7.952671 TCCGTATCTAGATTCATTTTAGTGCT 58.047 34.615 11.25 0.00 0.00 4.40
3623 5020 9.074576 TCCGTATCTAGATTCATTTTAGTGCTA 57.925 33.333 11.25 0.00 0.00 3.49
3624 5021 9.347934 CCGTATCTAGATTCATTTTAGTGCTAG 57.652 37.037 11.25 0.00 0.00 3.42
3632 5029 9.717942 AGATTCATTTTAGTGCTAGATACATCC 57.282 33.333 0.00 0.00 0.00 3.51
3633 5030 7.946655 TTCATTTTAGTGCTAGATACATCCG 57.053 36.000 0.00 0.00 0.00 4.18
3634 5031 7.050970 TCATTTTAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
3635 5032 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
3636 5033 8.803235 TCATTTTAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
3652 5049 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3653 5050 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3654 5051 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3655 5052 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3656 5053 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3657 5054 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
3668 5065 9.746711 CAAATCTAAGACAAGTAATTCAGAACG 57.253 33.333 0.00 0.00 0.00 3.95
3669 5066 8.480643 AATCTAAGACAAGTAATTCAGAACGG 57.519 34.615 0.00 0.00 0.00 4.44
3670 5067 7.223260 TCTAAGACAAGTAATTCAGAACGGA 57.777 36.000 0.00 0.00 0.00 4.69
3671 5068 7.313646 TCTAAGACAAGTAATTCAGAACGGAG 58.686 38.462 0.00 0.00 0.00 4.63
3672 5069 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
3673 5070 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3674 5071 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3675 5072 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3676 5073 3.442076 AGTAATTCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
3677 5074 4.607239 AGTAATTCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
3678 5075 3.889520 AATTCAGAACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
3679 5076 2.599408 TTCAGAACGGAGGGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
3686 5083 0.175989 CGGAGGGAGTACTTGAAGCC 59.824 60.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.907230 GAGAGGGGCCAGTCAAGTCT 60.907 60.000 4.39 0.0 0.00 3.24
196 214 1.204146 GTTGAGGATGCAGGTAGGGA 58.796 55.000 0.00 0.0 0.00 4.20
244 262 5.364157 GCCATATAGGGATCGGTTAGAGATT 59.636 44.000 7.83 0.0 38.09 2.40
527 548 7.959658 ACAAATCCTATCACCATCATTTCAA 57.040 32.000 0.00 0.0 0.00 2.69
695 716 8.506168 TTAATCAAACGATAGAATTCCAAGCT 57.494 30.769 0.65 0.0 41.38 3.74
843 932 2.478894 CAGTGCGTTCGTACCAGAATTT 59.521 45.455 9.49 0.0 32.25 1.82
1123 1213 0.326264 GGTGCTGATCTTCACCCTGT 59.674 55.000 19.75 0.0 45.26 4.00
1898 2003 9.826574 ACAACTAGTCACTAGATACAAAACAAA 57.173 29.630 19.25 0.0 37.49 2.83
1953 2058 1.346395 TCACGGCCACTGATTACTTGT 59.654 47.619 2.24 0.0 0.00 3.16
2338 2443 5.935945 TCAACCAAAAGTCAGATCCTACAA 58.064 37.500 0.00 0.0 0.00 2.41
2361 2466 3.168035 TGGCCTACATCACCAAAACAT 57.832 42.857 3.32 0.0 0.00 2.71
2603 2711 1.586154 GAAACCACATCAGCCCCACG 61.586 60.000 0.00 0.0 0.00 4.94
3008 3117 2.544267 GAGCAGTAGCAAAACAACGAGT 59.456 45.455 0.00 0.0 45.49 4.18
3337 4733 6.633500 AAGCAGTAGTAAAAACTCATGCAA 57.367 33.333 13.87 0.0 35.22 4.08
3465 4862 5.042593 GTCATGTCATGCAAAGTTCAAACA 58.957 37.500 8.03 0.0 0.00 2.83
3561 4958 3.986277 TCCAAGACAAGTAACTCGGAAC 58.014 45.455 0.00 0.0 0.00 3.62
3562 4959 4.884668 ATCCAAGACAAGTAACTCGGAA 57.115 40.909 0.00 0.0 0.00 4.30
3563 4960 4.884668 AATCCAAGACAAGTAACTCGGA 57.115 40.909 0.00 0.0 0.00 4.55
3564 4961 7.042335 AGATAAATCCAAGACAAGTAACTCGG 58.958 38.462 0.00 0.0 0.00 4.63
3565 4962 9.239002 CTAGATAAATCCAAGACAAGTAACTCG 57.761 37.037 0.00 0.0 0.00 4.18
3594 4991 9.698309 CACTAAAATGAATCTAGATACGGATGT 57.302 33.333 5.46 0.0 0.00 3.06
3595 4992 8.651588 GCACTAAAATGAATCTAGATACGGATG 58.348 37.037 5.46 0.0 0.00 3.51
3596 4993 8.589338 AGCACTAAAATGAATCTAGATACGGAT 58.411 33.333 5.46 0.0 0.00 4.18
3597 4994 7.952671 AGCACTAAAATGAATCTAGATACGGA 58.047 34.615 5.46 0.0 0.00 4.69
3598 4995 9.347934 CTAGCACTAAAATGAATCTAGATACGG 57.652 37.037 5.46 0.0 0.00 4.02
3606 5003 9.717942 GGATGTATCTAGCACTAAAATGAATCT 57.282 33.333 0.00 0.0 0.00 2.40
3607 5004 8.651588 CGGATGTATCTAGCACTAAAATGAATC 58.348 37.037 0.00 0.0 0.00 2.52
3608 5005 8.150945 ACGGATGTATCTAGCACTAAAATGAAT 58.849 33.333 0.00 0.0 0.00 2.57
3609 5006 7.497595 ACGGATGTATCTAGCACTAAAATGAA 58.502 34.615 0.00 0.0 0.00 2.57
3610 5007 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.0 0.00 2.57
3611 5008 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.0 36.56 2.32
3626 5023 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.0 34.45 2.29
3627 5024 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.0 0.00 3.06
3628 5025 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.0 0.00 3.51
3629 5026 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.0 0.00 4.18
3630 5027 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.0 0.00 4.69
3631 5028 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.0 0.00 4.02
3642 5039 9.746711 CGTTCTGAATTACTTGTCTTAGATTTG 57.253 33.333 0.00 0.0 0.00 2.32
3643 5040 8.936864 CCGTTCTGAATTACTTGTCTTAGATTT 58.063 33.333 0.00 0.0 0.00 2.17
3644 5041 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.0 0.00 2.40
3645 5042 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.0 0.00 1.98
3646 5043 7.223260 TCCGTTCTGAATTACTTGTCTTAGA 57.777 36.000 0.00 0.0 0.00 2.10
3647 5044 6.531948 CCTCCGTTCTGAATTACTTGTCTTAG 59.468 42.308 0.00 0.0 0.00 2.18
3648 5045 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.0 0.00 2.10
3649 5046 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.0 0.00 3.01
3650 5047 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.0 0.00 3.41
3651 5048 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.0 0.00 3.18
3652 5049 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.0 0.00 3.16
3653 5050 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.0 0.00 3.16
3654 5051 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.0 0.00 2.24
3655 5052 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.0 0.00 2.24
3656 5053 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.0 0.00 1.89
3657 5054 4.607239 AGTACTCCCTCCGTTCTGAATTA 58.393 43.478 0.00 0.0 0.00 1.40
3658 5055 3.442076 AGTACTCCCTCCGTTCTGAATT 58.558 45.455 0.00 0.0 0.00 2.17
3659 5056 3.103080 AGTACTCCCTCCGTTCTGAAT 57.897 47.619 0.00 0.0 0.00 2.57
3660 5057 2.561419 CAAGTACTCCCTCCGTTCTGAA 59.439 50.000 0.00 0.0 0.00 3.02
3661 5058 2.168496 CAAGTACTCCCTCCGTTCTGA 58.832 52.381 0.00 0.0 0.00 3.27
3662 5059 2.168496 TCAAGTACTCCCTCCGTTCTG 58.832 52.381 0.00 0.0 0.00 3.02
3663 5060 2.599408 TCAAGTACTCCCTCCGTTCT 57.401 50.000 0.00 0.0 0.00 3.01
3664 5061 2.674462 GCTTCAAGTACTCCCTCCGTTC 60.674 54.545 0.00 0.0 0.00 3.95
3665 5062 1.275573 GCTTCAAGTACTCCCTCCGTT 59.724 52.381 0.00 0.0 0.00 4.44
3666 5063 0.896226 GCTTCAAGTACTCCCTCCGT 59.104 55.000 0.00 0.0 0.00 4.69
3667 5064 0.175989 GGCTTCAAGTACTCCCTCCG 59.824 60.000 0.00 0.0 0.00 4.63
3668 5065 0.175989 CGGCTTCAAGTACTCCCTCC 59.824 60.000 0.00 0.0 0.00 4.30
3669 5066 0.896226 ACGGCTTCAAGTACTCCCTC 59.104 55.000 0.00 0.0 0.00 4.30
3670 5067 0.608640 CACGGCTTCAAGTACTCCCT 59.391 55.000 0.00 0.0 0.00 4.20
3671 5068 0.391263 CCACGGCTTCAAGTACTCCC 60.391 60.000 0.00 0.0 0.00 4.30
3672 5069 0.391263 CCCACGGCTTCAAGTACTCC 60.391 60.000 0.00 0.0 0.00 3.85
3673 5070 0.320697 ACCCACGGCTTCAAGTACTC 59.679 55.000 0.00 0.0 0.00 2.59
3674 5071 0.763035 AACCCACGGCTTCAAGTACT 59.237 50.000 0.00 0.0 0.00 2.73
3675 5072 2.460757 TAACCCACGGCTTCAAGTAC 57.539 50.000 0.00 0.0 0.00 2.73
3676 5073 3.244630 ACATTAACCCACGGCTTCAAGTA 60.245 43.478 0.00 0.0 0.00 2.24
3677 5074 2.159382 CATTAACCCACGGCTTCAAGT 58.841 47.619 0.00 0.0 0.00 3.16
3678 5075 2.095263 CACATTAACCCACGGCTTCAAG 60.095 50.000 0.00 0.0 0.00 3.02
3679 5076 1.883275 CACATTAACCCACGGCTTCAA 59.117 47.619 0.00 0.0 0.00 2.69
3686 5083 4.233789 CAAAATCACCACATTAACCCACG 58.766 43.478 0.00 0.0 0.00 4.94


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

AutoCloner maintained by Alex Coulton.