Multiple sequence alignment - TraesCS4B01G205000

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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 TraesCS4B01G205000 chr4B 100.000 4167 0 0 1 4167 437070637 437074803 0.000000e+00 7696.0
1 TraesCS4B01G205000 chr4B 80.672 714 126 9 1 706 44463912 44464621 1.020000e-150 544.0
2 TraesCS4B01G205000 chr4B 100.000 76 0 0 3948 4023 437074490 437074565 1.560000e-29 141.0
3 TraesCS4B01G205000 chr4B 100.000 76 0 0 3854 3929 437074584 437074659 1.560000e-29 141.0
4 TraesCS4B01G205000 chr4D 94.095 3150 95 29 706 3801 353519906 353523018 0.000000e+00 4702.0
5 TraesCS4B01G205000 chr4D 96.689 151 4 1 3921 4070 353523069 353523219 2.490000e-62 250.0
6 TraesCS4B01G205000 chr4D 97.368 76 2 0 3854 3929 353523097 353523172 3.380000e-26 130.0
7 TraesCS4B01G205000 chr4D 100.000 36 0 0 3819 3854 353523017 353523052 2.690000e-07 67.6
8 TraesCS4B01G205000 chr4A 92.128 3214 130 35 706 3853 111295482 111292326 0.000000e+00 4420.0
9 TraesCS4B01G205000 chr4A 94.667 225 8 2 3924 4148 111292305 111292085 3.080000e-91 346.0
10 TraesCS4B01G205000 chr4A 96.053 76 3 0 3854 3929 111292281 111292206 1.570000e-24 124.0
11 TraesCS4B01G205000 chr6D 90.860 558 41 7 154 708 5607646 5608196 0.000000e+00 739.0
12 TraesCS4B01G205000 chr6B 82.113 710 117 9 7 709 252818756 252818050 2.140000e-167 599.0
13 TraesCS4B01G205000 chr6B 83.571 420 66 3 290 707 529711625 529711207 1.400000e-104 390.0
14 TraesCS4B01G205000 chr1D 81.066 713 125 8 1 706 433112907 433113616 1.010000e-155 560.0
15 TraesCS4B01G205000 chr2B 80.140 715 131 8 1 707 788500290 788501001 1.330000e-144 523.0
16 TraesCS4B01G205000 chr3B 80.112 714 131 8 1 706 764745763 764746473 4.770000e-144 521.0
17 TraesCS4B01G205000 chr7D 80.763 655 120 3 1 650 589245370 589246023 1.340000e-139 507.0
18 TraesCS4B01G205000 chr6A 79.694 719 130 13 1 708 454691715 454692428 4.810000e-139 505.0
19 TraesCS4B01G205000 chr2D 79.416 753 85 33 1370 2062 568462574 568463316 6.310000e-128 468.0
20 TraesCS4B01G205000 chr5D 78.890 739 98 34 1370 2065 543635580 543634857 8.220000e-122 448.0
21 TraesCS4B01G205000 chr5A 81.908 304 38 10 1556 1845 11788792 11789092 1.500000e-59 241.0


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 TraesCS4B01G205000 chr4B 437070637 437074803 4166 False 2659.333333 7696 100.000000 1 4167 3 chr4B.!!$F2 4166
1 TraesCS4B01G205000 chr4B 44463912 44464621 709 False 544.000000 544 80.672000 1 706 1 chr4B.!!$F1 705
2 TraesCS4B01G205000 chr4D 353519906 353523219 3313 False 1287.400000 4702 97.038000 706 4070 4 chr4D.!!$F1 3364
3 TraesCS4B01G205000 chr4A 111292085 111295482 3397 True 1630.000000 4420 94.282667 706 4148 3 chr4A.!!$R1 3442
4 TraesCS4B01G205000 chr6D 5607646 5608196 550 False 739.000000 739 90.860000 154 708 1 chr6D.!!$F1 554
5 TraesCS4B01G205000 chr6B 252818050 252818756 706 True 599.000000 599 82.113000 7 709 1 chr6B.!!$R1 702
6 TraesCS4B01G205000 chr1D 433112907 433113616 709 False 560.000000 560 81.066000 1 706 1 chr1D.!!$F1 705
7 TraesCS4B01G205000 chr2B 788500290 788501001 711 False 523.000000 523 80.140000 1 707 1 chr2B.!!$F1 706
8 TraesCS4B01G205000 chr3B 764745763 764746473 710 False 521.000000 521 80.112000 1 706 1 chr3B.!!$F1 705
9 TraesCS4B01G205000 chr7D 589245370 589246023 653 False 507.000000 507 80.763000 1 650 1 chr7D.!!$F1 649
10 TraesCS4B01G205000 chr6A 454691715 454692428 713 False 505.000000 505 79.694000 1 708 1 chr6A.!!$F1 707
11 TraesCS4B01G205000 chr2D 568462574 568463316 742 False 468.000000 468 79.416000 1370 2062 1 chr2D.!!$F1 692
12 TraesCS4B01G205000 chr5D 543634857 543635580 723 True 448.000000 448 78.890000 1370 2065 1 chr5D.!!$R1 695

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
592 597 0.034476 GGCCAACTATAGCCGTACCC 59.966 60.000 0.00 0.0 39.87 3.69 F
1092 1130 1.433879 CCTCGACATGTCCCTCGAC 59.566 63.158 20.03 0.0 39.66 4.20 F
2197 2322 0.593128 GTGTGTTCTGTGTGATGCCC 59.407 55.000 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1732 1.394917 CTAGCACGACCAAATCACAGC 59.605 52.381 0.00 0.0 0.00 4.40 R
2329 2454 1.674221 GCTGGAGCAGTAGGAGTGTTG 60.674 57.143 0.00 0.0 41.59 3.33 R
3366 3517 0.038251 TCATGATAGATCGGCGGCAC 60.038 55.000 10.53 0.0 0.00 5.01 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
43 44 2.236395 ACATGGTAAGAAGGTTCCTCCG 59.764 50.000 0.00 0.00 41.99 4.63
52 53 0.613777 AGGTTCCTCCGGTTCATGTC 59.386 55.000 0.00 0.00 41.99 3.06
72 73 3.807622 GTCACAGTCGATTTCTTGGACAA 59.192 43.478 0.00 0.00 33.18 3.18
93 98 4.576216 ACTACTATCAGTCAGATTGGCG 57.424 45.455 0.00 0.00 38.19 5.69
96 101 1.414181 CTATCAGTCAGATTGGCGGGT 59.586 52.381 0.00 0.00 38.19 5.28
106 111 0.252197 ATTGGCGGGTAGGTTCTCAC 59.748 55.000 0.00 0.00 0.00 3.51
120 125 4.646572 GGTTCTCACCTGAAGAGATTGTT 58.353 43.478 0.00 0.00 41.42 2.83
159 164 2.757124 GGCTACCCCTCCCATGGTG 61.757 68.421 11.73 2.15 36.04 4.17
170 175 0.392998 CCCATGGTGGAGAAACCGAG 60.393 60.000 11.73 0.00 43.73 4.63
211 216 2.551287 CCGAAACCACAACCAGGTCATA 60.551 50.000 0.00 0.00 38.76 2.15
279 284 2.262471 CTGCTGGAATGGTGCTTCGC 62.262 60.000 0.00 0.00 0.00 4.70
312 317 5.392487 CGGTCATATCATCTTCTCTGCGTAT 60.392 44.000 0.00 0.00 0.00 3.06
321 326 2.757686 TCTCTGCGTATCGTGTGATC 57.242 50.000 0.00 0.00 35.99 2.92
350 355 0.035458 AACGACTCCTTGGAAGCAGG 59.965 55.000 0.00 0.00 0.00 4.85
403 408 4.161565 TGACTGTCCAACACTCTACACTTT 59.838 41.667 5.17 0.00 0.00 2.66
415 420 5.975344 CACTCTACACTTTCAGTTGTCGTTA 59.025 40.000 0.00 0.00 0.00 3.18
454 459 2.535732 GCGCTCTCTTGCTTATTGAACG 60.536 50.000 0.00 0.00 0.00 3.95
457 462 3.861840 CTCTCTTGCTTATTGAACGGGA 58.138 45.455 0.00 0.00 0.00 5.14
491 496 4.443621 TCGGCGTATGATCATTTGGTTAA 58.556 39.130 14.65 0.00 0.00 2.01
592 597 0.034476 GGCCAACTATAGCCGTACCC 59.966 60.000 0.00 0.00 39.87 3.69
629 634 2.741092 GTTGACCTCGGCTCCACA 59.259 61.111 0.00 0.00 0.00 4.17
673 678 8.202137 GGCCTCTTGATTGTAACACTATTACTA 58.798 37.037 0.00 0.00 0.00 1.82
674 679 9.032420 GCCTCTTGATTGTAACACTATTACTAC 57.968 37.037 0.00 0.00 0.00 2.73
696 701 8.676020 ACTACTTAATAAAACTCCCTTTCCCTT 58.324 33.333 0.00 0.00 0.00 3.95
745 750 3.979101 AAACTGGTTTGGCATAATGGG 57.021 42.857 0.00 0.00 0.00 4.00
1092 1130 1.433879 CCTCGACATGTCCCTCGAC 59.566 63.158 20.03 0.00 39.66 4.20
1588 1626 4.065088 TCCAGTTGTTGCTCTCATGTAAC 58.935 43.478 0.00 0.00 34.03 2.50
1639 1681 5.622346 AGAATCTCATAGTTTCCCTGGAC 57.378 43.478 0.00 0.00 0.00 4.02
1690 1732 0.671781 GCACAGGCTCAGTACCACAG 60.672 60.000 0.00 0.00 36.96 3.66
1814 1894 0.764890 TGGAAGGGTGTGACCTCTTG 59.235 55.000 0.00 0.00 40.87 3.02
1835 1915 1.533731 ACTGGCGTGGTTATGTTTTCG 59.466 47.619 0.00 0.00 0.00 3.46
1841 1921 3.669557 GCGTGGTTATGTTTTCGATTGCT 60.670 43.478 0.00 0.00 0.00 3.91
1855 1960 2.612672 CGATTGCTCTACGGTAGTCTCA 59.387 50.000 14.45 8.41 0.00 3.27
1856 1961 3.303461 CGATTGCTCTACGGTAGTCTCAG 60.303 52.174 14.45 6.21 0.00 3.35
1861 1966 3.427773 GCTCTACGGTAGTCTCAGTTTGG 60.428 52.174 14.45 0.00 0.00 3.28
1879 1991 7.807433 TCAGTTTGGTTCGTTTAATTGATGATG 59.193 33.333 0.00 0.00 0.00 3.07
1880 1992 6.586082 AGTTTGGTTCGTTTAATTGATGATGC 59.414 34.615 0.00 0.00 0.00 3.91
2143 2268 3.532232 TGGGAGGTCTAAGGTACTGATCT 59.468 47.826 0.00 0.00 40.86 2.75
2146 2271 5.163066 GGGAGGTCTAAGGTACTGATCTAGT 60.163 48.000 0.00 0.00 40.86 2.57
2197 2322 0.593128 GTGTGTTCTGTGTGATGCCC 59.407 55.000 0.00 0.00 0.00 5.36
2209 2334 3.435671 GTGTGATGCCCAACAGTACTTAC 59.564 47.826 0.00 0.00 0.00 2.34
2329 2454 8.097662 CCTATGAAAATAGAGATACTTGGGACC 58.902 40.741 0.00 0.00 0.00 4.46
2445 2570 9.328845 ACATATTTGTGGATTCAATTTATTGCC 57.671 29.630 0.00 0.00 34.67 4.52
2447 2572 7.852971 ATTTGTGGATTCAATTTATTGCCAG 57.147 32.000 0.00 0.00 37.68 4.85
2537 2662 5.762711 TGGATGGTGAATTGGTGATAATACG 59.237 40.000 0.00 0.00 0.00 3.06
2539 2664 6.073222 GGATGGTGAATTGGTGATAATACGAC 60.073 42.308 0.00 0.00 0.00 4.34
2563 2701 7.749666 ACTGCAGAGGTGTTCCATTATATATT 58.250 34.615 23.35 0.00 35.89 1.28
2605 2744 7.229907 TGACATTATATAACAGTAGGTGCTCGA 59.770 37.037 0.00 0.00 0.00 4.04
2820 2960 8.712285 TTGTCTGTTAGTAATAGATTTTCCCG 57.288 34.615 11.94 0.00 31.11 5.14
2826 2966 8.266473 TGTTAGTAATAGATTTTCCCGCCTTAA 58.734 33.333 0.00 0.00 0.00 1.85
2891 3031 3.077359 GCTAGTTTGCCACAGAACAGAT 58.923 45.455 0.00 0.00 0.00 2.90
3059 3199 1.295792 GCAGACCGCCGAATAAATCA 58.704 50.000 0.00 0.00 32.94 2.57
3203 3344 8.500753 TTACTGAATTGTATGGGTTATGTGTC 57.499 34.615 0.00 0.00 0.00 3.67
3324 3473 1.062488 AGGACCACCCAAGTTGCTCT 61.062 55.000 0.00 0.00 37.41 4.09
3357 3506 9.383519 GAAAGTTATTGAAGATGTATGAGGTGA 57.616 33.333 0.00 0.00 0.00 4.02
3366 3517 5.678583 AGATGTATGAGGTGAACATTCCTG 58.321 41.667 0.00 0.00 34.09 3.86
3374 3525 3.039202 GAACATTCCTGTGCCGCCG 62.039 63.158 0.00 0.00 35.22 6.46
3432 3583 6.377146 TGGTGATCAAGCTAAACCCTTATTTC 59.623 38.462 0.00 0.00 0.00 2.17
3458 3609 1.903404 CTTTGGGCGCTGTTTCCCT 60.903 57.895 7.64 0.00 43.04 4.20
3516 3667 4.965200 AGAGGTATGTTTCCCTATCTGC 57.035 45.455 0.00 0.00 0.00 4.26
3731 3886 6.842437 TGGTTATTGTGGCTTTGCTAATTA 57.158 33.333 0.00 0.00 0.00 1.40
3742 3897 5.163519 GGCTTTGCTAATTATGCTTCTTCCA 60.164 40.000 7.94 0.00 0.00 3.53
3791 3946 2.161012 TCTTCACGTACCGAGTCACATC 59.839 50.000 0.00 0.00 0.00 3.06
3854 4009 3.657727 TCTTCCTTCTTCAGGGGTCAATT 59.342 43.478 0.00 0.00 44.12 2.32
3856 4011 4.569719 TCCTTCTTCAGGGGTCAATTAC 57.430 45.455 0.00 0.00 44.12 1.89
3857 4012 4.175962 TCCTTCTTCAGGGGTCAATTACT 58.824 43.478 0.00 0.00 44.12 2.24
3858 4013 4.019321 TCCTTCTTCAGGGGTCAATTACTG 60.019 45.833 0.00 0.00 44.12 2.74
3859 4014 4.019321 CCTTCTTCAGGGGTCAATTACTGA 60.019 45.833 0.00 0.00 39.39 3.41
3860 4015 5.514834 CCTTCTTCAGGGGTCAATTACTGAA 60.515 44.000 0.00 0.00 44.87 3.02
3863 4018 5.576563 TTCAGGGGTCAATTACTGAAGAA 57.423 39.130 0.00 0.00 42.95 2.52
3864 4019 5.165961 TCAGGGGTCAATTACTGAAGAAG 57.834 43.478 0.00 0.00 37.06 2.85
3865 4020 3.691609 CAGGGGTCAATTACTGAAGAAGC 59.308 47.826 0.00 0.00 35.22 3.86
3868 4023 4.706962 GGGGTCAATTACTGAAGAAGCATT 59.293 41.667 0.00 0.00 35.22 3.56
3870 4025 6.377146 GGGGTCAATTACTGAAGAAGCATTAA 59.623 38.462 0.00 0.00 35.22 1.40
3871 4026 7.415653 GGGGTCAATTACTGAAGAAGCATTAAG 60.416 40.741 0.00 0.00 35.22 1.85
3872 4027 7.415653 GGGTCAATTACTGAAGAAGCATTAAGG 60.416 40.741 0.00 0.00 35.22 2.69
3873 4028 7.121315 GGTCAATTACTGAAGAAGCATTAAGGT 59.879 37.037 0.00 0.00 35.22 3.50
3874 4029 7.965107 GTCAATTACTGAAGAAGCATTAAGGTG 59.035 37.037 0.00 0.00 35.22 4.00
3875 4030 5.880054 TTACTGAAGAAGCATTAAGGTGC 57.120 39.130 0.00 0.00 45.38 5.01
3902 4057 3.564235 TGCTTTGCAATCTGCTAACAG 57.436 42.857 16.64 3.54 45.31 3.16
3903 4058 2.886523 TGCTTTGCAATCTGCTAACAGT 59.113 40.909 16.64 0.00 45.31 3.55
3904 4059 3.318839 TGCTTTGCAATCTGCTAACAGTT 59.681 39.130 16.64 0.00 45.31 3.16
3905 4060 4.518590 TGCTTTGCAATCTGCTAACAGTTA 59.481 37.500 16.64 0.00 45.31 2.24
3906 4061 5.009510 TGCTTTGCAATCTGCTAACAGTTAA 59.990 36.000 16.64 0.00 45.31 2.01
3907 4062 5.570589 GCTTTGCAATCTGCTAACAGTTAAG 59.429 40.000 0.00 0.00 45.31 1.85
3908 4063 5.627499 TTGCAATCTGCTAACAGTTAAGG 57.373 39.130 0.00 0.00 45.31 2.69
3909 4064 4.009675 TGCAATCTGCTAACAGTTAAGGG 58.990 43.478 0.00 0.00 45.31 3.95
3910 4065 4.010349 GCAATCTGCTAACAGTTAAGGGT 58.990 43.478 0.00 0.00 44.77 4.34
3911 4066 4.459337 GCAATCTGCTAACAGTTAAGGGTT 59.541 41.667 0.00 0.00 44.77 4.11
3912 4067 5.619981 GCAATCTGCTAACAGTTAAGGGTTG 60.620 44.000 0.00 2.42 44.77 3.77
3913 4068 4.699925 TCTGCTAACAGTTAAGGGTTGT 57.300 40.909 0.00 0.00 44.77 3.32
3914 4069 4.638304 TCTGCTAACAGTTAAGGGTTGTC 58.362 43.478 0.00 0.00 44.77 3.18
3915 4070 4.101898 TCTGCTAACAGTTAAGGGTTGTCA 59.898 41.667 0.00 0.82 44.77 3.58
3916 4071 4.783055 TGCTAACAGTTAAGGGTTGTCAA 58.217 39.130 0.00 0.00 0.00 3.18
3917 4072 5.381757 TGCTAACAGTTAAGGGTTGTCAAT 58.618 37.500 0.00 0.00 0.00 2.57
3918 4073 5.830991 TGCTAACAGTTAAGGGTTGTCAATT 59.169 36.000 0.00 0.00 0.00 2.32
3919 4074 6.149633 GCTAACAGTTAAGGGTTGTCAATTG 58.850 40.000 0.00 0.00 0.00 2.32
3922 4077 4.959839 ACAGTTAAGGGTTGTCAATTGGTT 59.040 37.500 5.42 0.00 0.00 3.67
4095 4251 5.126061 GCTGACTTCATTTATGATGGTTGGT 59.874 40.000 9.55 0.00 36.56 3.67
4096 4252 6.513806 TGACTTCATTTATGATGGTTGGTG 57.486 37.500 9.55 0.00 36.56 4.17
4097 4253 5.418524 TGACTTCATTTATGATGGTTGGTGG 59.581 40.000 9.55 0.00 36.56 4.61
4098 4254 4.711355 ACTTCATTTATGATGGTTGGTGGG 59.289 41.667 9.55 0.00 36.56 4.61
4099 4255 3.030291 TCATTTATGATGGTTGGTGGGC 58.970 45.455 0.00 0.00 0.00 5.36
4100 4256 1.859302 TTTATGATGGTTGGTGGGCC 58.141 50.000 0.00 0.00 0.00 5.80
4101 4257 1.006813 TTATGATGGTTGGTGGGCCT 58.993 50.000 4.53 0.00 35.27 5.19
4103 4259 0.116940 ATGATGGTTGGTGGGCCTTT 59.883 50.000 4.53 0.00 35.27 3.11
4104 4260 0.541764 TGATGGTTGGTGGGCCTTTC 60.542 55.000 4.53 0.00 35.27 2.62
4105 4261 1.229177 ATGGTTGGTGGGCCTTTCC 60.229 57.895 4.53 5.54 35.27 3.13
4134 4290 8.579850 TGAAATTCAACTAGGCATCAAAGTAT 57.420 30.769 0.00 0.00 0.00 2.12
4148 4304 7.418942 GGCATCAAAGTATTATTTGGAACCCAT 60.419 37.037 0.00 0.00 39.99 4.00
4149 4305 7.653311 GCATCAAAGTATTATTTGGAACCCATC 59.347 37.037 0.00 0.00 39.99 3.51
4150 4306 7.328277 TCAAAGTATTATTTGGAACCCATCG 57.672 36.000 0.00 0.00 39.99 3.84
4151 4307 6.887545 TCAAAGTATTATTTGGAACCCATCGT 59.112 34.615 0.00 0.00 39.99 3.73
4152 4308 6.937436 AAGTATTATTTGGAACCCATCGTC 57.063 37.500 0.00 0.00 31.53 4.20
4153 4309 6.248569 AGTATTATTTGGAACCCATCGTCT 57.751 37.500 0.00 0.00 31.53 4.18
4154 4310 7.369551 AGTATTATTTGGAACCCATCGTCTA 57.630 36.000 0.00 0.00 31.53 2.59
4155 4311 7.974504 AGTATTATTTGGAACCCATCGTCTAT 58.025 34.615 0.00 0.00 31.53 1.98
4156 4312 9.096823 AGTATTATTTGGAACCCATCGTCTATA 57.903 33.333 0.00 0.00 31.53 1.31
4157 4313 9.886132 GTATTATTTGGAACCCATCGTCTATAT 57.114 33.333 0.00 0.00 31.53 0.86
4159 4315 6.688073 ATTTGGAACCCATCGTCTATATCT 57.312 37.500 0.00 0.00 31.53 1.98
4160 4316 6.494666 TTTGGAACCCATCGTCTATATCTT 57.505 37.500 0.00 0.00 31.53 2.40
4161 4317 6.494666 TTGGAACCCATCGTCTATATCTTT 57.505 37.500 0.00 0.00 31.53 2.52
4162 4318 5.853936 TGGAACCCATCGTCTATATCTTTG 58.146 41.667 0.00 0.00 0.00 2.77
4163 4319 5.365605 TGGAACCCATCGTCTATATCTTTGT 59.634 40.000 0.00 0.00 0.00 2.83
4164 4320 6.126883 TGGAACCCATCGTCTATATCTTTGTT 60.127 38.462 0.00 0.00 0.00 2.83
4165 4321 6.424207 GGAACCCATCGTCTATATCTTTGTTC 59.576 42.308 0.00 0.00 0.00 3.18
4166 4322 5.855045 ACCCATCGTCTATATCTTTGTTCC 58.145 41.667 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.997021 AGAAATCGACTGTGACATGAACC 59.003 43.478 0.00 0.00 0.00 3.62
52 53 3.809832 AGTTGTCCAAGAAATCGACTGTG 59.190 43.478 0.00 0.00 0.00 3.66
72 73 3.319405 CCGCCAATCTGACTGATAGTAGT 59.681 47.826 0.00 0.00 34.45 2.73
93 98 2.498078 CTCTTCAGGTGAGAACCTACCC 59.502 54.545 0.00 0.00 38.22 3.69
96 101 5.087323 ACAATCTCTTCAGGTGAGAACCTA 58.913 41.667 0.00 0.00 42.84 3.08
106 111 6.476378 TCTTCCCTTTAACAATCTCTTCAGG 58.524 40.000 0.00 0.00 0.00 3.86
111 116 5.196695 GGCATCTTCCCTTTAACAATCTCT 58.803 41.667 0.00 0.00 0.00 3.10
114 119 5.595952 AGATGGCATCTTCCCTTTAACAATC 59.404 40.000 24.01 0.00 35.76 2.67
159 164 0.391793 CTTGAGGCCTCGGTTTCTCC 60.392 60.000 27.43 1.45 0.00 3.71
211 216 1.524002 CATCCACCGAGAGTGCCAT 59.476 57.895 0.00 0.00 45.83 4.40
279 284 0.526739 TGATATGACCGGCGTTGTCG 60.527 55.000 6.01 0.00 35.46 4.35
312 317 0.678950 TGCAGTGGAAGATCACACGA 59.321 50.000 0.00 0.00 42.25 4.35
321 326 0.034059 AGGAGTCGTTGCAGTGGAAG 59.966 55.000 0.00 0.00 0.00 3.46
350 355 2.613595 TCTTGCATGGTCGCATGTATTC 59.386 45.455 0.00 0.00 42.62 1.75
371 376 1.956477 GTTGGACAGTCAAAGCCATGT 59.044 47.619 2.17 0.00 0.00 3.21
382 387 4.161565 TGAAAGTGTAGAGTGTTGGACAGT 59.838 41.667 0.00 0.00 33.77 3.55
403 408 3.928727 ATCCGACTTAACGACAACTGA 57.071 42.857 0.00 0.00 35.09 3.41
415 420 2.009774 CGCTTCCAATGAATCCGACTT 58.990 47.619 0.00 0.00 30.94 3.01
454 459 2.202676 CGAGCGCTCAAGACTCCC 60.203 66.667 34.69 7.57 0.00 4.30
479 484 9.525826 ACTCTTTGATCTCTTTAACCAAATGAT 57.474 29.630 0.00 0.00 0.00 2.45
480 485 8.924511 ACTCTTTGATCTCTTTAACCAAATGA 57.075 30.769 0.00 0.00 0.00 2.57
629 634 3.117888 AGGCCACAAATCCTCGATACAAT 60.118 43.478 5.01 0.00 0.00 2.71
673 678 7.532199 TCAAGGGAAAGGGAGTTTTATTAAGT 58.468 34.615 0.00 0.00 0.00 2.24
674 679 8.417273 TTCAAGGGAAAGGGAGTTTTATTAAG 57.583 34.615 0.00 0.00 0.00 1.85
745 750 4.330347 GCTCGTTCTTCCTTCCTACAAATC 59.670 45.833 0.00 0.00 0.00 2.17
816 824 1.644786 GACGGGGATTGTTTCGGCTG 61.645 60.000 0.00 0.00 0.00 4.85
817 825 1.376812 GACGGGGATTGTTTCGGCT 60.377 57.895 0.00 0.00 0.00 5.52
818 826 2.746803 CGACGGGGATTGTTTCGGC 61.747 63.158 0.00 0.00 0.00 5.54
819 827 2.746803 GCGACGGGGATTGTTTCGG 61.747 63.158 0.00 0.00 0.00 4.30
820 828 2.782615 GCGACGGGGATTGTTTCG 59.217 61.111 0.00 0.00 0.00 3.46
821 829 2.782615 CGCGACGGGGATTGTTTC 59.217 61.111 0.00 0.00 0.00 2.78
1020 1058 3.682292 CTGGCGCTAGGGTTGGGAC 62.682 68.421 13.78 0.00 0.00 4.46
1092 1130 3.681417 TCTTGTTGCTCTTGATGATGTCG 59.319 43.478 0.00 0.00 0.00 4.35
1588 1626 5.063880 ACCAACTACTAAGAAGCAACCAAG 58.936 41.667 0.00 0.00 0.00 3.61
1690 1732 1.394917 CTAGCACGACCAAATCACAGC 59.605 52.381 0.00 0.00 0.00 4.40
1814 1894 2.412325 CGAAAACATAACCACGCCAGTC 60.412 50.000 0.00 0.00 0.00 3.51
1835 1915 3.628487 ACTGAGACTACCGTAGAGCAATC 59.372 47.826 12.66 0.00 0.00 2.67
1841 1921 3.759581 ACCAAACTGAGACTACCGTAGA 58.240 45.455 12.66 0.00 0.00 2.59
1855 1960 6.586082 GCATCATCAATTAAACGAACCAAACT 59.414 34.615 0.00 0.00 0.00 2.66
1856 1961 6.586082 AGCATCATCAATTAAACGAACCAAAC 59.414 34.615 0.00 0.00 0.00 2.93
1861 1966 6.949877 GCAAAAGCATCATCAATTAAACGAAC 59.050 34.615 0.00 0.00 0.00 3.95
1879 1991 8.862550 AAGTAAGCAATAAGATATGCAAAAGC 57.137 30.769 0.00 0.00 44.95 3.51
2112 2237 2.572284 GACCTCCCACTTCGGTCG 59.428 66.667 0.00 0.00 38.00 4.79
2169 2294 2.945008 ACACAGAACACACACATGGAAG 59.055 45.455 0.00 0.00 0.00 3.46
2329 2454 1.674221 GCTGGAGCAGTAGGAGTGTTG 60.674 57.143 0.00 0.00 41.59 3.33
2445 2570 7.383102 ACAGGCAAATTCAGATACTTTACTG 57.617 36.000 0.00 0.00 35.72 2.74
2447 2572 7.062255 GCAAACAGGCAAATTCAGATACTTTAC 59.938 37.037 0.00 0.00 0.00 2.01
2577 2715 9.542462 GAGCACCTACTGTTATATAATGTCAAA 57.458 33.333 0.00 0.00 0.00 2.69
2578 2716 7.865889 CGAGCACCTACTGTTATATAATGTCAA 59.134 37.037 0.00 0.00 0.00 3.18
2579 2717 7.229907 TCGAGCACCTACTGTTATATAATGTCA 59.770 37.037 0.00 0.00 0.00 3.58
2820 2960 2.758009 TGAAGTGGTGTACGTTAAGGC 58.242 47.619 0.00 0.00 0.00 4.35
2826 2966 5.117584 TGTAACAAATGAAGTGGTGTACGT 58.882 37.500 0.00 0.00 0.00 3.57
3047 3187 5.101628 TGCAAAGATGTTGATTTATTCGGC 58.898 37.500 0.00 0.00 0.00 5.54
3059 3199 4.970662 ATATCAACGCTGCAAAGATGTT 57.029 36.364 0.00 0.00 0.00 2.71
3203 3344 6.829298 TCCACTCAACTCTAGTTCTATGTAGG 59.171 42.308 0.00 0.00 35.83 3.18
3324 3473 7.218228 ACATCTTCAATAACTTTCACATGCA 57.782 32.000 0.00 0.00 0.00 3.96
3357 3506 2.819984 ATCGGCGGCACAGGAATGTT 62.820 55.000 10.53 0.00 0.00 2.71
3366 3517 0.038251 TCATGATAGATCGGCGGCAC 60.038 55.000 10.53 0.00 0.00 5.01
3374 3525 7.160049 TCTGAATTTCAGCCTCATGATAGATC 58.840 38.462 19.53 0.00 43.95 2.75
3449 3600 1.734465 GATCGTTCAGCAGGGAAACAG 59.266 52.381 0.00 0.00 0.00 3.16
3458 3609 4.754618 TGAAGCTTAAAAGATCGTTCAGCA 59.245 37.500 20.31 4.90 0.00 4.41
3731 3886 3.056322 GCACCTTGATTTGGAAGAAGCAT 60.056 43.478 0.00 0.00 0.00 3.79
3742 3897 5.726980 TTGCTAGATTTGCACCTTGATTT 57.273 34.783 0.00 0.00 40.40 2.17
3791 3946 0.692419 ACAGTATCCCTCCAGCTGGG 60.692 60.000 32.23 21.66 45.90 4.45
3804 3959 7.855904 CACGCAAAACTTCTAAAAGAACAGTAT 59.144 33.333 0.00 0.00 36.30 2.12
3854 4009 4.905429 TGCACCTTAATGCTTCTTCAGTA 58.095 39.130 2.92 0.00 46.28 2.74
3856 4011 4.771590 TTGCACCTTAATGCTTCTTCAG 57.228 40.909 2.92 0.00 46.28 3.02
3857 4012 5.477984 AGATTTGCACCTTAATGCTTCTTCA 59.522 36.000 2.92 0.00 46.28 3.02
3858 4013 5.958955 AGATTTGCACCTTAATGCTTCTTC 58.041 37.500 2.92 0.00 46.28 2.87
3859 4014 5.990120 AGATTTGCACCTTAATGCTTCTT 57.010 34.783 2.92 0.00 46.28 2.52
3860 4015 5.717119 CAAGATTTGCACCTTAATGCTTCT 58.283 37.500 2.92 0.88 46.28 2.85
3888 4043 4.010349 ACCCTTAACTGTTAGCAGATTGC 58.990 43.478 14.09 0.00 45.28 3.56
3889 4044 5.473504 ACAACCCTTAACTGTTAGCAGATTG 59.526 40.000 14.09 7.93 45.28 2.67
3890 4045 5.631119 ACAACCCTTAACTGTTAGCAGATT 58.369 37.500 14.09 6.61 45.28 2.40
3891 4046 5.221843 TGACAACCCTTAACTGTTAGCAGAT 60.222 40.000 14.09 3.91 45.28 2.90
3892 4047 4.101898 TGACAACCCTTAACTGTTAGCAGA 59.898 41.667 14.09 0.00 45.28 4.26
3894 4049 4.425180 TGACAACCCTTAACTGTTAGCA 57.575 40.909 0.00 0.00 0.00 3.49
3895 4050 5.959618 ATTGACAACCCTTAACTGTTAGC 57.040 39.130 0.00 0.00 0.00 3.09
3896 4051 6.264518 ACCAATTGACAACCCTTAACTGTTAG 59.735 38.462 7.12 0.00 0.00 2.34
3897 4052 6.130569 ACCAATTGACAACCCTTAACTGTTA 58.869 36.000 7.12 0.00 0.00 2.41
3898 4053 4.959839 ACCAATTGACAACCCTTAACTGTT 59.040 37.500 7.12 0.00 0.00 3.16
3899 4054 4.542697 ACCAATTGACAACCCTTAACTGT 58.457 39.130 7.12 0.00 0.00 3.55
3900 4055 5.529581 AACCAATTGACAACCCTTAACTG 57.470 39.130 7.12 0.00 0.00 3.16
3901 4056 5.163353 CCAAACCAATTGACAACCCTTAACT 60.163 40.000 7.12 0.00 41.85 2.24
3902 4057 5.053811 CCAAACCAATTGACAACCCTTAAC 58.946 41.667 7.12 0.00 41.85 2.01
3903 4058 4.717280 ACCAAACCAATTGACAACCCTTAA 59.283 37.500 7.12 0.00 41.85 1.85
3904 4059 4.100189 CACCAAACCAATTGACAACCCTTA 59.900 41.667 7.12 0.00 41.85 2.69
3905 4060 3.111484 ACCAAACCAATTGACAACCCTT 58.889 40.909 7.12 0.00 41.85 3.95
3906 4061 2.433970 CACCAAACCAATTGACAACCCT 59.566 45.455 7.12 0.00 41.85 4.34
3907 4062 2.484594 CCACCAAACCAATTGACAACCC 60.485 50.000 7.12 0.00 41.85 4.11
3908 4063 2.432510 TCCACCAAACCAATTGACAACC 59.567 45.455 7.12 0.00 41.85 3.77
3909 4064 3.810310 TCCACCAAACCAATTGACAAC 57.190 42.857 7.12 0.00 41.85 3.32
3910 4065 4.500545 CGAATCCACCAAACCAATTGACAA 60.501 41.667 7.12 0.00 41.85 3.18
3911 4066 3.005261 CGAATCCACCAAACCAATTGACA 59.995 43.478 7.12 0.00 41.85 3.58
3912 4067 3.574614 CGAATCCACCAAACCAATTGAC 58.425 45.455 7.12 0.00 41.85 3.18
3913 4068 2.029470 GCGAATCCACCAAACCAATTGA 60.029 45.455 7.12 0.00 41.85 2.57
3914 4069 2.029110 AGCGAATCCACCAAACCAATTG 60.029 45.455 0.00 0.00 38.84 2.32
3915 4070 2.247358 AGCGAATCCACCAAACCAATT 58.753 42.857 0.00 0.00 0.00 2.32
3916 4071 1.923356 AGCGAATCCACCAAACCAAT 58.077 45.000 0.00 0.00 0.00 3.16
3917 4072 2.224670 ACTAGCGAATCCACCAAACCAA 60.225 45.455 0.00 0.00 0.00 3.67
3918 4073 1.349688 ACTAGCGAATCCACCAAACCA 59.650 47.619 0.00 0.00 0.00 3.67
3919 4074 2.109425 ACTAGCGAATCCACCAAACC 57.891 50.000 0.00 0.00 0.00 3.27
3922 4077 1.339631 CCCAACTAGCGAATCCACCAA 60.340 52.381 0.00 0.00 0.00 3.67
3984 4140 5.631119 ACAACCCTTAACTGTTAGCAGATT 58.369 37.500 14.09 6.61 45.28 2.40
4095 4251 3.209091 TTTCAAACGGAAAGGCCCA 57.791 47.368 0.00 0.00 40.51 5.36
4103 4259 4.138290 TGCCTAGTTGAATTTCAAACGGA 58.862 39.130 13.21 0.79 38.22 4.69
4104 4260 4.497473 TGCCTAGTTGAATTTCAAACGG 57.503 40.909 13.21 13.63 38.22 4.44
4105 4261 5.698832 TGATGCCTAGTTGAATTTCAAACG 58.301 37.500 13.21 5.29 38.22 3.60
4134 4290 8.202461 AGATATAGACGATGGGTTCCAAATAA 57.798 34.615 0.00 0.00 36.95 1.40


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

AutoCloner maintained by Alex Coulton.