Multiple sequence alignment - TraesCS5D01G503500

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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 TraesCS5D01G503500 chr5D 100.000 4376 0 0 1 4376 530403680 530408055 0.000000e+00 8082.0
1 TraesCS5D01G503500 chr5D 89.355 667 53 15 3714 4376 530346956 530346304 0.000000e+00 822.0
2 TraesCS5D01G503500 chr5D 88.140 371 38 3 4006 4376 530169685 530169321 1.870000e-118 436.0
3 TraesCS5D01G503500 chr5D 87.871 371 39 3 4006 4376 530301862 530301498 8.690000e-117 431.0
4 TraesCS5D01G503500 chr5D 81.319 455 60 16 3279 3717 530360920 530360475 3.240000e-91 346.0
5 TraesCS5D01G503500 chr5D 85.938 256 36 0 3442 3697 530302818 530302563 1.550000e-69 274.0
6 TraesCS5D01G503500 chr5D 83.333 276 46 0 3442 3717 530221024 530220749 5.620000e-64 255.0
7 TraesCS5D01G503500 chr5D 80.303 330 43 15 3714 4035 530302178 530301863 3.400000e-56 230.0
8 TraesCS5D01G503500 chr5D 81.982 222 29 6 3821 4035 530169903 530169686 1.250000e-40 178.0
9 TraesCS5D01G503500 chr5B 93.907 2429 103 26 1038 3432 669481645 669484062 0.000000e+00 3624.0
10 TraesCS5D01G503500 chr5B 87.782 1064 69 25 1 1036 669480483 669481513 0.000000e+00 1188.0
11 TraesCS5D01G503500 chr5B 93.899 672 29 5 3714 4376 669484808 669485476 0.000000e+00 1003.0
12 TraesCS5D01G503500 chr5B 94.502 291 13 2 3431 3718 669484166 669484456 3.110000e-121 446.0
13 TraesCS5D01G503500 chr5B 86.807 379 44 3 3998 4376 669429887 669429515 6.770000e-113 418.0
14 TraesCS5D01G503500 chr5B 84.058 276 44 0 3442 3717 669434850 669434575 2.590000e-67 267.0
15 TraesCS5D01G503500 chr5B 85.115 262 38 1 3436 3697 669439053 669438793 2.590000e-67 267.0
16 TraesCS5D01G503500 chr5B 83.969 262 42 0 3436 3697 669443249 669442988 7.270000e-63 252.0
17 TraesCS5D01G503500 chr5B 80.631 222 32 6 3821 4035 669430097 669429880 1.260000e-35 161.0
18 TraesCS5D01G503500 chr5B 81.651 109 18 2 3714 3821 669446232 669446125 6.030000e-14 89.8
19 TraesCS5D01G503500 chr5A 91.549 2118 130 25 1038 3132 658597409 658599500 0.000000e+00 2874.0
20 TraesCS5D01G503500 chr5A 88.060 804 48 25 1 778 658596308 658597089 0.000000e+00 909.0
21 TraesCS5D01G503500 chr5A 87.500 664 73 10 3714 4374 658494499 658493843 0.000000e+00 758.0
22 TraesCS5D01G503500 chr5A 89.209 278 19 3 4009 4282 658599943 658600213 1.950000e-88 337.0
23 TraesCS5D01G503500 chr5A 93.519 216 12 1 821 1036 658597087 658597300 1.960000e-83 320.0
24 TraesCS5D01G503500 chr5A 79.579 475 66 21 3266 3717 658501983 658501517 1.180000e-80 311.0
25 TraesCS5D01G503500 chr5A 93.264 193 13 0 3436 3628 658599736 658599928 7.160000e-73 285.0
26 TraesCS5D01G503500 chr5A 82.222 270 42 3 4107 4376 658487204 658486941 1.220000e-55 228.0
27 TraesCS5D01G503500 chr5A 82.422 256 45 0 3442 3697 658490590 658490335 1.580000e-54 224.0
28 TraesCS5D01G503500 chr2A 78.571 672 122 14 3716 4376 758371909 758372569 1.450000e-114 424.0
29 TraesCS5D01G503500 chr2D 81.641 512 81 7 3874 4376 627843342 627842835 3.150000e-111 412.0
30 TraesCS5D01G503500 chr6B 83.158 380 49 6 4006 4376 26145302 26144929 2.520000e-87 333.0
31 TraesCS5D01G503500 chr2B 78.817 524 75 12 3874 4376 770100765 770100257 1.960000e-83 320.0
32 TraesCS5D01G503500 chr6D 91.781 73 6 0 3873 3945 14360502 14360574 7.740000e-18 102.0


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 TraesCS5D01G503500 chr5D 530403680 530408055 4375 False 8082.000000 8082 100.00000 1 4376 1 chr5D.!!$F1 4375
1 TraesCS5D01G503500 chr5D 530346304 530346956 652 True 822.000000 822 89.35500 3714 4376 1 chr5D.!!$R2 662
2 TraesCS5D01G503500 chr5D 530301498 530302818 1320 True 311.666667 431 84.70400 3442 4376 3 chr5D.!!$R5 934
3 TraesCS5D01G503500 chr5D 530169321 530169903 582 True 307.000000 436 85.06100 3821 4376 2 chr5D.!!$R4 555
4 TraesCS5D01G503500 chr5B 669480483 669485476 4993 False 1565.250000 3624 92.52250 1 4376 4 chr5B.!!$F1 4375
5 TraesCS5D01G503500 chr5B 669429515 669430097 582 True 289.500000 418 83.71900 3821 4376 2 chr5B.!!$R1 555
6 TraesCS5D01G503500 chr5B 669434575 669446232 11657 True 218.950000 267 83.69825 3436 3821 4 chr5B.!!$R2 385
7 TraesCS5D01G503500 chr5A 658596308 658600213 3905 False 945.000000 2874 91.12020 1 4282 5 chr5A.!!$F1 4281
8 TraesCS5D01G503500 chr5A 658486941 658494499 7558 True 403.333333 758 84.04800 3442 4376 3 chr5A.!!$R2 934
9 TraesCS5D01G503500 chr2A 758371909 758372569 660 False 424.000000 424 78.57100 3716 4376 1 chr2A.!!$F1 660
10 TraesCS5D01G503500 chr2D 627842835 627843342 507 True 412.000000 412 81.64100 3874 4376 1 chr2D.!!$R1 502
11 TraesCS5D01G503500 chr2B 770100257 770100765 508 True 320.000000 320 78.81700 3874 4376 1 chr2B.!!$R1 502

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
438 479 0.033796 CCATGGTTGGTCTGCAGGAT 60.034 55.0 15.13 0.0 38.3 3.24 F
707 758 0.250513 AAATCCTGACAGACGGCCTC 59.749 55.0 3.32 0.0 0.0 4.70 F
2631 2838 0.462047 CGCAGACCCCTTACATCCAC 60.462 60.0 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2413 7.008810 GTGTGAAGAAGATCGAATACTTCAGAC 59.991 40.741 23.89 23.89 46.18 3.51 R
2699 2906 1.066605 GCATGAACATGGCTGCCTTAG 59.933 52.381 21.03 11.76 39.16 2.18 R
3628 7372 0.654683 GCTGATTGTCCTCGATGTGC 59.345 55.000 0.00 0.00 0.00 4.57 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
118 123 2.688666 CCTGGGCAGGGTAGAGCA 60.689 66.667 0.00 0.00 44.87 4.26
119 124 2.739996 CCTGGGCAGGGTAGAGCAG 61.740 68.421 0.00 0.00 44.87 4.24
120 125 1.687146 CTGGGCAGGGTAGAGCAGA 60.687 63.158 0.00 0.00 0.00 4.26
129 134 0.179113 GGTAGAGCAGAGCAGAGCAC 60.179 60.000 0.00 0.00 0.00 4.40
134 144 1.671704 GCAGAGCAGAGCACAGCTT 60.672 57.895 2.06 0.00 39.88 3.74
346 386 1.660167 GCCCACACGGAGGTAAATAC 58.340 55.000 0.00 0.00 0.00 1.89
372 412 2.999063 GCTGCCCCTGTTGCCATT 60.999 61.111 0.00 0.00 0.00 3.16
390 430 4.320641 GCCATTCGCCAACAAGTAGTTTTA 60.321 41.667 0.00 0.00 38.74 1.52
430 471 2.092323 GGTTAGCTTCCATGGTTGGTC 58.908 52.381 12.58 1.05 44.06 4.02
433 474 0.610232 AGCTTCCATGGTTGGTCTGC 60.610 55.000 12.58 6.89 44.06 4.26
436 477 0.251297 TTCCATGGTTGGTCTGCAGG 60.251 55.000 15.13 0.00 44.06 4.85
438 479 0.033796 CCATGGTTGGTCTGCAGGAT 60.034 55.000 15.13 0.00 38.30 3.24
439 480 1.100510 CATGGTTGGTCTGCAGGATG 58.899 55.000 15.13 1.79 40.87 3.51
440 481 0.700564 ATGGTTGGTCTGCAGGATGT 59.299 50.000 15.13 0.00 39.31 3.06
441 482 1.357137 TGGTTGGTCTGCAGGATGTA 58.643 50.000 15.13 0.00 39.31 2.29
457 498 8.773645 TGCAGGATGTATACAGATTTTATTTCG 58.226 33.333 11.91 0.00 39.31 3.46
493 534 5.116084 TGTCATTAGAGGGGAAGGAATTG 57.884 43.478 0.00 0.00 0.00 2.32
495 536 4.884164 GTCATTAGAGGGGAAGGAATTGTG 59.116 45.833 0.00 0.00 0.00 3.33
497 538 4.569719 TTAGAGGGGAAGGAATTGTGTC 57.430 45.455 0.00 0.00 0.00 3.67
498 539 1.279271 AGAGGGGAAGGAATTGTGTCG 59.721 52.381 0.00 0.00 0.00 4.35
499 540 1.003233 GAGGGGAAGGAATTGTGTCGT 59.997 52.381 0.00 0.00 0.00 4.34
500 541 1.003233 AGGGGAAGGAATTGTGTCGTC 59.997 52.381 0.00 0.00 0.00 4.20
503 544 3.146847 GGGAAGGAATTGTGTCGTCTTT 58.853 45.455 0.00 0.00 0.00 2.52
523 564 8.060679 CGTCTTTTTCATCTGCTTACATATCTG 58.939 37.037 0.00 0.00 0.00 2.90
578 619 7.766278 CCTGGTAATATCACCTACATAATCTGC 59.234 40.741 0.00 0.00 39.50 4.26
579 620 8.435931 TGGTAATATCACCTACATAATCTGCT 57.564 34.615 0.00 0.00 39.50 4.24
606 651 0.675083 TGCAAAAGCATGGTGACTGG 59.325 50.000 0.00 0.00 0.00 4.00
635 680 7.630082 ACTGCTAAGGAACAATCAGGTAATAA 58.370 34.615 0.00 0.00 0.00 1.40
651 696 5.425630 GGTAATAACACCTAGACAACCTGG 58.574 45.833 0.00 0.00 35.55 4.45
695 746 8.394971 TGATAGCAACAATATGGTAAATCCTG 57.605 34.615 0.00 0.00 36.90 3.86
702 753 6.049149 ACAATATGGTAAATCCTGACAGACG 58.951 40.000 3.32 0.00 37.07 4.18
707 758 0.250513 AAATCCTGACAGACGGCCTC 59.749 55.000 3.32 0.00 0.00 4.70
768 819 5.260424 ACATATGGTGGTCATTGTTTGCTA 58.740 37.500 7.80 0.00 37.30 3.49
800 851 3.306472 AAGTGGGCACAAGACCTTTTA 57.694 42.857 0.00 0.00 46.30 1.52
819 870 2.533266 AGTATTGGCACCTGATAGCG 57.467 50.000 0.00 0.00 0.00 4.26
838 889 8.876790 TGATAGCGCTTTGATAATAATCTGATG 58.123 33.333 18.68 0.00 32.93 3.07
848 899 9.662947 TTGATAATAATCTGATGGCTGACATAG 57.337 33.333 0.00 0.00 34.88 2.23
872 923 8.331931 AGTAGAACAGGATAACCATAATTCCA 57.668 34.615 0.00 0.00 38.94 3.53
891 942 6.522625 TTCCATATTTTTCATGCCGAAAGA 57.477 33.333 0.00 0.00 44.32 2.52
907 958 3.433615 CGAAAGAGGTCATGTTGAAGGTC 59.566 47.826 0.00 0.00 0.00 3.85
929 980 5.293569 GTCGAATGGATCACGAATAACCTTT 59.706 40.000 0.00 0.00 37.77 3.11
1036 1087 7.915397 ACTCATGTGTTATTGTTGTGAAAAGTC 59.085 33.333 0.00 0.00 0.00 3.01
1082 1263 1.999735 TCTCAGCGCAACTATTTTCCG 59.000 47.619 11.47 0.00 0.00 4.30
1124 1305 2.473609 TGCTTAGTTGAACAAGTACGCG 59.526 45.455 18.69 3.53 41.55 6.01
1125 1306 2.720891 GCTTAGTTGAACAAGTACGCGC 60.721 50.000 5.73 0.00 33.71 6.86
1126 1307 1.421382 TAGTTGAACAAGTACGCGCC 58.579 50.000 5.73 0.00 0.00 6.53
1127 1308 1.154727 GTTGAACAAGTACGCGCCG 60.155 57.895 5.73 0.00 0.00 6.46
1152 1333 4.069304 CGGACAAGTAAATGGGAGTTCAA 58.931 43.478 0.00 0.00 0.00 2.69
1395 1584 8.438676 AATGGTGTCTAGTATGAAATAGTTGC 57.561 34.615 0.00 0.00 33.67 4.17
1977 2174 3.608008 GCATATTAAGCAAGAAGAGCCGC 60.608 47.826 0.00 0.00 0.00 6.53
2119 2317 7.568349 AGATCTGCATGTGATAACCTTCTTTA 58.432 34.615 0.00 0.00 0.00 1.85
2213 2413 8.781196 AGCATTATATTATGACTGCAACTTCTG 58.219 33.333 5.90 0.00 32.18 3.02
2289 2489 6.422333 TGAACATCCAAGATTACTAATGGCA 58.578 36.000 0.00 0.00 32.87 4.92
2496 2703 2.224402 ACACAAGAGTTCTCTTCTGCCC 60.224 50.000 14.50 0.00 0.00 5.36
2622 2829 1.789576 ATGTTTTCCCGCAGACCCCT 61.790 55.000 0.00 0.00 0.00 4.79
2631 2838 0.462047 CGCAGACCCCTTACATCCAC 60.462 60.000 0.00 0.00 0.00 4.02
2699 2906 3.798202 AGCTTCTTGAATGACGGGATAC 58.202 45.455 0.00 0.00 0.00 2.24
2706 2913 3.035363 TGAATGACGGGATACTAAGGCA 58.965 45.455 0.00 0.00 0.00 4.75
2718 2925 2.372264 ACTAAGGCAGCCATGTTCATG 58.628 47.619 15.80 5.88 0.00 3.07
2725 2932 1.380246 GCCATGTTCATGCCTCCCA 60.380 57.895 7.21 0.00 0.00 4.37
2733 2940 1.203441 TCATGCCTCCCAGCTGTTCT 61.203 55.000 13.81 0.00 0.00 3.01
2836 3043 0.967380 AGCCGAAAAGCATTGGAGGG 60.967 55.000 0.00 0.00 34.23 4.30
2894 3102 2.007608 GATCTAGGAACCGGTTTGTGC 58.992 52.381 23.22 8.36 0.00 4.57
3016 3232 9.653287 TGTTGTGTATTTTAGTAGAATGGAGAG 57.347 33.333 0.00 0.00 0.00 3.20
3033 3249 8.421249 AATGGAGAGAATTTGGTTATTGACAA 57.579 30.769 0.00 0.00 0.00 3.18
3045 3261 6.454795 TGGTTATTGACAATTTCCTTTCTGC 58.545 36.000 5.89 0.00 0.00 4.26
3134 3353 1.002087 ACATCTCGTTGAAGACCACCC 59.998 52.381 0.00 0.00 0.00 4.61
3135 3354 1.276421 CATCTCGTTGAAGACCACCCT 59.724 52.381 0.00 0.00 0.00 4.34
3144 3363 1.001406 GAAGACCACCCTGTCTGTCAG 59.999 57.143 0.00 0.00 44.68 3.51
3153 3372 2.037772 CCCTGTCTGTCAGTTAGCAACT 59.962 50.000 0.00 0.00 44.06 3.16
3260 3507 7.134163 TGAAGCAAATGTGATAATATTCGCAG 58.866 34.615 0.00 0.00 39.33 5.18
3261 3508 6.866010 AGCAAATGTGATAATATTCGCAGA 57.134 33.333 0.00 0.00 39.33 4.26
3262 3509 6.662616 AGCAAATGTGATAATATTCGCAGAC 58.337 36.000 0.00 0.00 39.33 3.51
3263 3510 6.260714 AGCAAATGTGATAATATTCGCAGACA 59.739 34.615 0.00 0.00 39.33 3.41
3265 3512 7.592533 GCAAATGTGATAATATTCGCAGACAAT 59.407 33.333 0.00 0.00 39.33 2.71
3266 3513 8.898792 CAAATGTGATAATATTCGCAGACAATG 58.101 33.333 0.00 0.00 39.33 2.82
3276 3523 2.858622 CAGACAATGCACCCGATGT 58.141 52.632 0.00 0.00 0.00 3.06
3290 3537 2.643551 CCGATGTCCATAACCTGCTTT 58.356 47.619 0.00 0.00 0.00 3.51
3291 3538 3.433031 CCCGATGTCCATAACCTGCTTTA 60.433 47.826 0.00 0.00 0.00 1.85
3293 3540 4.442893 CCGATGTCCATAACCTGCTTTAGA 60.443 45.833 0.00 0.00 0.00 2.10
3299 3548 4.288626 TCCATAACCTGCTTTAGAACCAGT 59.711 41.667 0.00 0.00 0.00 4.00
3311 3560 3.515602 AGAACCAGTCATGAAGGCTTT 57.484 42.857 13.86 3.81 0.00 3.51
3409 3658 8.766994 AATGGTAATGCAACTAGGAATGTTAT 57.233 30.769 0.00 0.00 0.00 1.89
3411 3660 7.342581 TGGTAATGCAACTAGGAATGTTATGA 58.657 34.615 0.00 0.00 0.00 2.15
3427 3676 0.246360 ATGACGAGTTCGACCATGCA 59.754 50.000 8.72 0.00 43.02 3.96
3628 7372 4.821589 GCAGCCGGAGTCGAAGGG 62.822 72.222 5.05 0.00 39.00 3.95
3634 7378 1.519455 CGGAGTCGAAGGGCACATC 60.519 63.158 0.00 0.00 39.00 3.06
3658 7405 0.908198 ACAATCAGCCTCTGGAGACC 59.092 55.000 0.00 0.00 31.51 3.85
3787 7911 4.286707 TGGATTGGGAGTAGAAAGATCGA 58.713 43.478 0.00 0.00 0.00 3.59
3798 7934 3.678717 AAGATCGACGACGCCACCG 62.679 63.158 0.00 0.00 39.58 4.94
3855 8256 1.144057 CGATCTTGTTCCCGAGGGG 59.856 63.158 8.53 0.00 46.11 4.79
3870 8271 2.521708 GGGGGAATTGGATGGCGG 60.522 66.667 0.00 0.00 0.00 6.13
4093 16053 3.861797 CTGTAGCCGCCGGGGATT 61.862 66.667 21.95 9.98 38.47 3.01
4101 16061 2.440065 GCCGGGGATTGTGATGCA 60.440 61.111 2.18 0.00 0.00 3.96
4198 17117 3.386237 GTGACGAGCAGGGCCTCT 61.386 66.667 0.95 3.77 0.00 3.69
4200 17119 3.386237 GACGAGCAGGGCCTCTGT 61.386 66.667 18.80 0.00 45.08 3.41
4227 17146 0.951558 GAGACGTGGTTGCCATTTGT 59.048 50.000 0.00 0.00 35.28 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 111 1.143620 CTGCTCTGCTCTACCCTGC 59.856 63.158 0.00 0.00 0.00 4.85
107 112 0.746063 CTCTGCTCTGCTCTACCCTG 59.254 60.000 0.00 0.00 0.00 4.45
108 113 1.042559 GCTCTGCTCTGCTCTACCCT 61.043 60.000 0.00 0.00 0.00 4.34
109 114 1.326213 TGCTCTGCTCTGCTCTACCC 61.326 60.000 0.00 0.00 0.00 3.69
110 115 0.179113 GTGCTCTGCTCTGCTCTACC 60.179 60.000 0.00 0.00 0.00 3.18
111 116 0.529833 TGTGCTCTGCTCTGCTCTAC 59.470 55.000 0.00 0.00 0.00 2.59
112 117 0.816373 CTGTGCTCTGCTCTGCTCTA 59.184 55.000 0.00 0.00 0.00 2.43
114 119 2.101835 GCTGTGCTCTGCTCTGCTC 61.102 63.158 10.03 0.00 41.36 4.26
115 120 2.047083 GCTGTGCTCTGCTCTGCT 60.047 61.111 10.03 0.00 41.36 4.24
116 121 1.637478 GAAGCTGTGCTCTGCTCTGC 61.637 60.000 18.64 12.97 45.59 4.26
117 122 1.020333 GGAAGCTGTGCTCTGCTCTG 61.020 60.000 18.64 0.00 45.59 3.35
118 123 1.296068 GGAAGCTGTGCTCTGCTCT 59.704 57.895 18.64 10.26 45.59 4.09
119 124 2.099431 CGGAAGCTGTGCTCTGCTC 61.099 63.158 18.64 12.47 45.59 4.26
172 183 1.227497 GATCCAAGGAGAGCAGCGG 60.227 63.158 0.00 0.00 0.00 5.52
372 412 3.189702 GGCATAAAACTACTTGTTGGCGA 59.810 43.478 0.00 0.00 39.13 5.54
390 430 1.610554 GAGTTTGCAGGCATGGGCAT 61.611 55.000 0.00 0.00 43.71 4.40
457 498 6.697892 CCTCTAATGACATCGGTAAGAGAAAC 59.302 42.308 10.75 0.00 32.57 2.78
493 534 4.474226 AAGCAGATGAAAAAGACGACAC 57.526 40.909 0.00 0.00 0.00 3.67
495 536 5.591643 TGTAAGCAGATGAAAAAGACGAC 57.408 39.130 0.00 0.00 0.00 4.34
497 538 8.060679 CAGATATGTAAGCAGATGAAAAAGACG 58.939 37.037 0.00 0.00 0.00 4.18
498 539 8.341173 CCAGATATGTAAGCAGATGAAAAAGAC 58.659 37.037 0.00 0.00 0.00 3.01
499 540 8.267183 TCCAGATATGTAAGCAGATGAAAAAGA 58.733 33.333 0.00 0.00 0.00 2.52
500 541 8.341173 GTCCAGATATGTAAGCAGATGAAAAAG 58.659 37.037 0.00 0.00 0.00 2.27
503 544 6.988580 CAGTCCAGATATGTAAGCAGATGAAA 59.011 38.462 0.00 0.00 0.00 2.69
523 564 7.600752 GTCTAATTAGCAGTTATCATCCAGTCC 59.399 40.741 7.67 0.00 0.00 3.85
594 639 1.002868 AGTCAGCCAGTCACCATGC 60.003 57.895 0.00 0.00 0.00 4.06
606 651 3.338249 TGATTGTTCCTTAGCAGTCAGC 58.662 45.455 0.00 0.00 46.19 4.26
635 680 3.255634 ACTACCAGGTTGTCTAGGTGT 57.744 47.619 0.00 0.00 35.62 4.16
651 696 9.058174 TGCTATCAGACTGTAGAAGATAACTAC 57.942 37.037 13.17 0.00 40.13 2.73
707 758 3.722147 AGATTAGCTGAGTGGCATTACG 58.278 45.455 0.00 0.00 34.17 3.18
800 851 1.541233 GCGCTATCAGGTGCCAATACT 60.541 52.381 0.00 0.00 36.81 2.12
819 870 7.040892 TGTCAGCCATCAGATTATTATCAAAGC 60.041 37.037 0.00 0.00 32.95 3.51
838 889 4.946478 ATCCTGTTCTACTATGTCAGCC 57.054 45.455 0.00 0.00 0.00 4.85
872 923 5.652014 TGACCTCTTTCGGCATGAAAAATAT 59.348 36.000 0.00 0.00 45.59 1.28
891 942 3.338249 CATTCGACCTTCAACATGACCT 58.662 45.455 0.00 0.00 0.00 3.85
907 958 5.734855 AAAGGTTATTCGTGATCCATTCG 57.265 39.130 0.00 0.00 0.00 3.34
1082 1263 5.098211 GCAGAACAGATAATTTTCCTGTGC 58.902 41.667 0.00 0.00 40.61 4.57
1124 1305 1.747745 ATTTACTTGTCCGGCCGGC 60.748 57.895 39.89 31.83 34.68 6.13
1125 1306 1.373590 CCATTTACTTGTCCGGCCGG 61.374 60.000 39.13 39.13 0.00 6.13
1126 1307 1.373590 CCCATTTACTTGTCCGGCCG 61.374 60.000 21.04 21.04 0.00 6.13
1127 1308 0.034863 TCCCATTTACTTGTCCGGCC 60.035 55.000 0.00 0.00 0.00 6.13
1152 1333 1.110442 CAGGAGGTCTTCGATCTGCT 58.890 55.000 0.00 0.00 42.06 4.24
1977 2174 9.345517 CACATCAAGTTTGGTTACATTGAATAG 57.654 33.333 0.00 0.00 33.91 1.73
2213 2413 7.008810 GTGTGAAGAAGATCGAATACTTCAGAC 59.991 40.741 23.89 23.89 46.18 3.51
2380 2581 9.331282 GTCTATTATTCTGAAAGTAACATGGCT 57.669 33.333 0.00 0.00 33.76 4.75
2622 2829 1.375853 GCCATGCAGCGTGGATGTAA 61.376 55.000 34.31 0.00 43.51 2.41
2699 2906 1.066605 GCATGAACATGGCTGCCTTAG 59.933 52.381 21.03 11.76 39.16 2.18
2725 2932 5.590259 ACAGTTTGTTGATAACAGAACAGCT 59.410 36.000 15.29 0.00 43.27 4.24
2836 3043 7.014422 AGAGAGCAATATACCCTGTGTACTAAC 59.986 40.741 0.00 0.00 30.62 2.34
3033 3249 7.890655 ACTTAAGGTAATGAGCAGAAAGGAAAT 59.109 33.333 7.53 0.00 0.00 2.17
3134 3353 8.571757 GCAGTATAGTTGCTAACTGACAGACAG 61.572 44.444 10.08 6.59 42.84 3.51
3135 3354 6.621613 CAGTATAGTTGCTAACTGACAGACA 58.378 40.000 10.08 0.00 42.84 3.41
3153 3372 7.556275 CCTTAATTTGGTCTTGGAAGCAGTATA 59.444 37.037 0.00 0.00 0.00 1.47
3162 3382 4.898861 AGCAAACCTTAATTTGGTCTTGGA 59.101 37.500 16.69 0.00 44.80 3.53
3260 3507 0.676466 TGGACATCGGGTGCATTGTC 60.676 55.000 0.00 0.00 43.49 3.18
3261 3508 1.378378 TGGACATCGGGTGCATTGT 59.622 52.632 0.00 0.00 43.49 2.71
3262 3509 4.317359 TGGACATCGGGTGCATTG 57.683 55.556 0.00 0.00 43.49 2.82
3266 3513 0.180406 AGGTTATGGACATCGGGTGC 59.820 55.000 0.00 0.00 38.51 5.01
3267 3514 1.953559 CAGGTTATGGACATCGGGTG 58.046 55.000 0.00 0.00 0.00 4.61
3268 3515 0.180406 GCAGGTTATGGACATCGGGT 59.820 55.000 0.00 0.00 0.00 5.28
3269 3516 0.469917 AGCAGGTTATGGACATCGGG 59.530 55.000 0.00 0.00 0.00 5.14
3271 3518 4.693283 TCTAAAGCAGGTTATGGACATCG 58.307 43.478 0.00 0.00 0.00 3.84
3272 3519 5.297029 GGTTCTAAAGCAGGTTATGGACATC 59.703 44.000 0.00 0.00 0.00 3.06
3273 3520 5.193679 GGTTCTAAAGCAGGTTATGGACAT 58.806 41.667 0.00 0.00 0.00 3.06
3274 3521 4.042311 TGGTTCTAAAGCAGGTTATGGACA 59.958 41.667 0.00 0.00 34.36 4.02
3276 3523 4.919774 TGGTTCTAAAGCAGGTTATGGA 57.080 40.909 0.00 0.00 34.36 3.41
3290 3537 4.565652 GGAAAGCCTTCATGACTGGTTCTA 60.566 45.833 13.57 0.00 32.75 2.10
3291 3538 3.416156 GAAAGCCTTCATGACTGGTTCT 58.584 45.455 13.57 3.11 0.00 3.01
3293 3540 2.108952 AGGAAAGCCTTCATGACTGGTT 59.891 45.455 13.57 8.53 43.90 3.67
3314 3563 5.217978 TCTTTAGCCGTTCTCCTTGTTAA 57.782 39.130 0.00 0.00 0.00 2.01
3317 3566 3.764237 TTCTTTAGCCGTTCTCCTTGT 57.236 42.857 0.00 0.00 0.00 3.16
3318 3567 3.813166 TGTTTCTTTAGCCGTTCTCCTTG 59.187 43.478 0.00 0.00 0.00 3.61
3321 3570 4.331992 GGTATGTTTCTTTAGCCGTTCTCC 59.668 45.833 0.00 0.00 0.00 3.71
3330 3579 9.750125 AGCTTTCTTTTTGGTATGTTTCTTTAG 57.250 29.630 0.00 0.00 0.00 1.85
3409 3658 0.032815 TTGCATGGTCGAACTCGTCA 59.967 50.000 0.33 0.35 40.80 4.35
3411 3660 0.033504 AGTTGCATGGTCGAACTCGT 59.966 50.000 0.33 0.00 40.80 4.18
3427 3676 4.510038 AACATCACGTACGTTCCTAGTT 57.490 40.909 20.23 15.45 0.00 2.24
3616 7360 1.519455 GATGTGCCCTTCGACTCCG 60.519 63.158 0.00 0.00 37.07 4.63
3628 7372 0.654683 GCTGATTGTCCTCGATGTGC 59.345 55.000 0.00 0.00 0.00 4.57
3709 7456 1.975680 GGGAGTCTGTACCTGGTTCAA 59.024 52.381 3.84 0.00 0.00 2.69
3855 8256 1.076339 TTCCCGCCATCCAATTCCC 60.076 57.895 0.00 0.00 0.00 3.97
3868 8269 1.079336 GTTCCGGTTCTCCTTCCCG 60.079 63.158 0.00 0.00 41.37 5.14
3870 8271 1.071857 AGTTGTTCCGGTTCTCCTTCC 59.928 52.381 0.00 0.00 0.00 3.46
4004 15932 3.869272 GCCGGCGTTCATCTGCAG 61.869 66.667 12.58 7.63 0.00 4.41


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

AutoCloner maintained by Alex Coulton.