Multiple sequence alignment - TraesCS6A01G119800

Loading Multiple Alignment...

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 TraesCS6A01G119800 chr6A 100.000 4010 0 0 1 4010 91430197 91426188 0.000000e+00 7406
1 TraesCS6A01G119800 chr6D 94.489 2504 93 20 568 3059 75377714 75375244 0.000000e+00 3818
2 TraesCS6A01G119800 chr6D 95.221 816 18 11 3211 4010 75375012 75374202 0.000000e+00 1271
3 TraesCS6A01G119800 chr6D 96.894 161 4 1 3052 3212 75375206 75375047 6.610000e-68 268
4 TraesCS6A01G119800 chr6B 93.720 2516 114 24 519 3024 149060519 149058038 0.000000e+00 3731
5 TraesCS6A01G119800 chr6B 83.754 357 23 19 3048 3379 149057927 149057581 5.030000e-79 305
6 TraesCS6A01G119800 chr6B 92.424 132 10 0 3854 3985 149056800 149056669 5.290000e-44 189
7 TraesCS6A01G119800 chr6B 90.789 76 4 1 3779 3851 149056906 149056831 9.170000e-17 99
8 TraesCS6A01G119800 chr7D 75.541 2032 436 47 1031 3021 535755406 535753395 0.000000e+00 942
9 TraesCS6A01G119800 chr1A 96.124 516 20 0 1 516 12126945 12127460 0.000000e+00 843
10 TraesCS6A01G119800 chr1A 94.391 517 28 1 1 516 222268717 222269233 0.000000e+00 793
11 TraesCS6A01G119800 chr7B 94.767 516 27 0 1 516 663194613 663195128 0.000000e+00 804
12 TraesCS6A01G119800 chr7B 94.574 516 28 0 1 516 428933850 428933335 0.000000e+00 798
13 TraesCS6A01G119800 chr7B 95.010 501 24 1 16 516 56357209 56357708 0.000000e+00 785
14 TraesCS6A01G119800 chr7B 94.004 517 30 1 1 516 713392623 713392107 0.000000e+00 782
15 TraesCS6A01G119800 chr7B 93.992 516 30 1 1 516 45326860 45326346 0.000000e+00 780
16 TraesCS6A01G119800 chr7B 93.411 516 34 0 1 516 131367843 131367328 0.000000e+00 765
17 TraesCS6A01G119800 chr2B 93.992 516 31 0 1 516 768546398 768545883 0.000000e+00 782


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 TraesCS6A01G119800 chr6A 91426188 91430197 4009 True 7406.000000 7406 100.000000 1 4010 1 chr6A.!!$R1 4009
1 TraesCS6A01G119800 chr6D 75374202 75377714 3512 True 1785.666667 3818 95.534667 568 4010 3 chr6D.!!$R1 3442
2 TraesCS6A01G119800 chr6B 149056669 149060519 3850 True 1081.000000 3731 90.171750 519 3985 4 chr6B.!!$R1 3466
3 TraesCS6A01G119800 chr7D 535753395 535755406 2011 True 942.000000 942 75.541000 1031 3021 1 chr7D.!!$R1 1990
4 TraesCS6A01G119800 chr1A 12126945 12127460 515 False 843.000000 843 96.124000 1 516 1 chr1A.!!$F1 515
5 TraesCS6A01G119800 chr1A 222268717 222269233 516 False 793.000000 793 94.391000 1 516 1 chr1A.!!$F2 515
6 TraesCS6A01G119800 chr7B 663194613 663195128 515 False 804.000000 804 94.767000 1 516 1 chr7B.!!$F2 515
7 TraesCS6A01G119800 chr7B 428933335 428933850 515 True 798.000000 798 94.574000 1 516 1 chr7B.!!$R3 515
8 TraesCS6A01G119800 chr7B 713392107 713392623 516 True 782.000000 782 94.004000 1 516 1 chr7B.!!$R4 515
9 TraesCS6A01G119800 chr7B 45326346 45326860 514 True 780.000000 780 93.992000 1 516 1 chr7B.!!$R1 515
10 TraesCS6A01G119800 chr7B 131367328 131367843 515 True 765.000000 765 93.411000 1 516 1 chr7B.!!$R2 515
11 TraesCS6A01G119800 chr2B 768545883 768546398 515 True 782.000000 782 93.992000 1 516 1 chr2B.!!$R1 515

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
854 871 0.036294 CGAAGAAACCCCACTCCCTC 60.036 60.0 0.00 0.0 0.0 4.3 F
1812 1866 0.174845 CTGACGACGCCCAGGAATTA 59.825 55.0 9.28 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2310 1.021390 CAAGGAGCCGGTTGCAGTAG 61.021 60.000 13.2 0.0 44.83 2.57 R
3060 3178 1.341679 ACAGCAATGCCCTCATCACAT 60.342 47.619 0.0 0.0 31.27 3.21 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
24 25 1.693627 CAGCCTACGTCTATCCCACT 58.306 55.000 0.00 0.00 0.00 4.00
169 171 2.446435 TGCTTCTTTAATCACCCTGCC 58.554 47.619 0.00 0.00 0.00 4.85
378 381 6.294176 CGGACAAGACAATTTCCAAATCTTCT 60.294 38.462 0.00 0.00 0.00 2.85
457 460 3.324556 CCATGTTGTTGGTTCCATTCCTT 59.675 43.478 0.00 0.00 31.74 3.36
516 519 3.666902 CGTAAAACTCCACGCAATGAAGG 60.667 47.826 0.00 0.00 0.00 3.46
517 520 2.270352 AAACTCCACGCAATGAAGGA 57.730 45.000 0.00 0.00 0.00 3.36
518 521 2.270352 AACTCCACGCAATGAAGGAA 57.730 45.000 0.00 0.00 0.00 3.36
519 522 2.270352 ACTCCACGCAATGAAGGAAA 57.730 45.000 0.00 0.00 0.00 3.13
520 523 2.582052 ACTCCACGCAATGAAGGAAAA 58.418 42.857 0.00 0.00 0.00 2.29
521 524 2.955660 ACTCCACGCAATGAAGGAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
555 558 2.100216 GTTTAGCGCATGTGCCCG 59.900 61.111 26.95 6.86 37.91 6.13
581 585 5.174035 CGTCGGTGAGCAGATAGAAAAATAG 59.826 44.000 0.00 0.00 0.00 1.73
585 589 6.978659 CGGTGAGCAGATAGAAAAATAGTGTA 59.021 38.462 0.00 0.00 0.00 2.90
586 590 7.491372 CGGTGAGCAGATAGAAAAATAGTGTAA 59.509 37.037 0.00 0.00 0.00 2.41
587 591 9.162764 GGTGAGCAGATAGAAAAATAGTGTAAA 57.837 33.333 0.00 0.00 0.00 2.01
639 643 2.095461 GTCCTTTCCTTTGGATGCTCC 58.905 52.381 0.00 0.00 36.96 4.70
660 672 3.199508 CCAAATCTCCTCTGACATCACCT 59.800 47.826 0.00 0.00 0.00 4.00
677 689 1.314581 CCTAAACGAAAACGCAAGCG 58.685 50.000 13.50 13.50 46.03 4.68
691 703 3.376935 AAGCGCCATCCTCCTGTCG 62.377 63.158 2.29 0.00 0.00 4.35
768 780 4.698625 AGTTCGTCGCCCCCTCCT 62.699 66.667 0.00 0.00 0.00 3.69
769 781 4.144703 GTTCGTCGCCCCCTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
834 851 1.202769 TCCTCCCAACCTAAACCCGG 61.203 60.000 0.00 0.00 0.00 5.73
839 856 1.303091 CCAACCTAAACCCGGCGAAG 61.303 60.000 9.30 0.92 0.00 3.79
840 857 0.320946 CAACCTAAACCCGGCGAAGA 60.321 55.000 9.30 0.00 0.00 2.87
841 858 0.397564 AACCTAAACCCGGCGAAGAA 59.602 50.000 9.30 0.00 0.00 2.52
842 859 0.397564 ACCTAAACCCGGCGAAGAAA 59.602 50.000 9.30 0.00 0.00 2.52
843 860 0.800631 CCTAAACCCGGCGAAGAAAC 59.199 55.000 9.30 0.00 0.00 2.78
844 861 0.800631 CTAAACCCGGCGAAGAAACC 59.199 55.000 9.30 0.00 0.00 3.27
845 862 0.606130 TAAACCCGGCGAAGAAACCC 60.606 55.000 9.30 0.00 0.00 4.11
846 863 3.855503 AACCCGGCGAAGAAACCCC 62.856 63.158 9.30 0.00 0.00 4.95
847 864 4.338710 CCCGGCGAAGAAACCCCA 62.339 66.667 9.30 0.00 0.00 4.96
848 865 3.053896 CCGGCGAAGAAACCCCAC 61.054 66.667 9.30 0.00 0.00 4.61
849 866 2.032071 CGGCGAAGAAACCCCACT 59.968 61.111 0.00 0.00 0.00 4.00
850 867 2.033194 CGGCGAAGAAACCCCACTC 61.033 63.158 0.00 0.00 0.00 3.51
851 868 1.674651 GGCGAAGAAACCCCACTCC 60.675 63.158 0.00 0.00 0.00 3.85
852 869 1.674651 GCGAAGAAACCCCACTCCC 60.675 63.158 0.00 0.00 0.00 4.30
853 870 2.067197 CGAAGAAACCCCACTCCCT 58.933 57.895 0.00 0.00 0.00 4.20
854 871 0.036294 CGAAGAAACCCCACTCCCTC 60.036 60.000 0.00 0.00 0.00 4.30
855 872 1.363246 GAAGAAACCCCACTCCCTCT 58.637 55.000 0.00 0.00 0.00 3.69
856 873 1.279558 GAAGAAACCCCACTCCCTCTC 59.720 57.143 0.00 0.00 0.00 3.20
857 874 0.905337 AGAAACCCCACTCCCTCTCG 60.905 60.000 0.00 0.00 0.00 4.04
858 875 2.523453 GAAACCCCACTCCCTCTCGC 62.523 65.000 0.00 0.00 0.00 5.03
859 876 3.547787 AACCCCACTCCCTCTCGCT 62.548 63.158 0.00 0.00 0.00 4.93
860 877 3.151022 CCCCACTCCCTCTCGCTC 61.151 72.222 0.00 0.00 0.00 5.03
861 878 3.151022 CCCACTCCCTCTCGCTCC 61.151 72.222 0.00 0.00 0.00 4.70
862 879 2.363018 CCACTCCCTCTCGCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
863 880 2.716017 CCACTCCCTCTCGCTCCAC 61.716 68.421 0.00 0.00 0.00 4.02
864 881 2.363147 ACTCCCTCTCGCTCCACC 60.363 66.667 0.00 0.00 0.00 4.61
865 882 3.522731 CTCCCTCTCGCTCCACCG 61.523 72.222 0.00 0.00 0.00 4.94
868 885 3.827898 CCTCTCGCTCCACCGGAC 61.828 72.222 9.46 0.00 0.00 4.79
869 886 4.180946 CTCTCGCTCCACCGGACG 62.181 72.222 9.46 3.64 0.00 4.79
893 910 3.064324 GCAGCCAGCCGTTTCCAT 61.064 61.111 0.00 0.00 37.23 3.41
919 952 1.701757 AGAGAGGGAGGGATCCGGA 60.702 63.158 6.61 6.61 0.00 5.14
988 1021 1.896465 AGGTTCTTTCACCCTCTCTCG 59.104 52.381 0.00 0.00 37.58 4.04
990 1023 0.608640 TTCTTTCACCCTCTCTCGCC 59.391 55.000 0.00 0.00 0.00 5.54
991 1024 0.541998 TCTTTCACCCTCTCTCGCCA 60.542 55.000 0.00 0.00 0.00 5.69
993 1026 2.154798 TTTCACCCTCTCTCGCCACG 62.155 60.000 0.00 0.00 0.00 4.94
1579 1621 3.074369 TCCTCGCCGAGCATTCCA 61.074 61.111 9.01 0.00 0.00 3.53
1797 1851 1.242076 ACTTGCACAATCCAGCTGAC 58.758 50.000 17.39 0.00 0.00 3.51
1803 1857 2.125512 AATCCAGCTGACGACGCC 60.126 61.111 17.39 0.00 0.00 5.68
1809 1863 4.373116 GCTGACGACGCCCAGGAA 62.373 66.667 16.35 0.00 0.00 3.36
1812 1866 0.174845 CTGACGACGCCCAGGAATTA 59.825 55.000 9.28 0.00 0.00 1.40
1828 1882 2.547123 ATTAGGCCCTGGGGTCGAGT 62.547 60.000 16.03 0.00 46.16 4.18
2116 2170 0.301687 GTGTGCGGATATTCAGTGCG 59.698 55.000 0.00 0.00 0.00 5.34
2256 2310 2.921754 CCTGGTCACTTTTATCGTCGAC 59.078 50.000 5.18 5.18 0.00 4.20
2373 2427 3.349006 CTTGCTGTCGCGGTGCTT 61.349 61.111 6.13 0.00 39.65 3.91
2535 2589 1.492176 GGTGATGTGTGGATCAGGGAT 59.508 52.381 0.00 0.00 32.92 3.85
2643 2697 1.073199 CTTGTTCTCCAAGGGCCGT 59.927 57.895 0.00 0.00 45.70 5.68
3167 3314 1.226974 CCTCCGCGTGTATGTGAGG 60.227 63.158 4.92 8.21 0.00 3.86
3188 3351 3.685272 GGTGCTGCCTAAGTTAACTTCTC 59.315 47.826 23.76 14.06 37.40 2.87
3189 3352 3.685272 GTGCTGCCTAAGTTAACTTCTCC 59.315 47.826 23.76 13.16 37.40 3.71
3190 3353 3.326588 TGCTGCCTAAGTTAACTTCTCCA 59.673 43.478 23.76 16.50 37.40 3.86
3191 3354 4.202419 TGCTGCCTAAGTTAACTTCTCCAA 60.202 41.667 23.76 5.89 37.40 3.53
3192 3355 4.944317 GCTGCCTAAGTTAACTTCTCCAAT 59.056 41.667 23.76 1.45 37.40 3.16
3194 3357 6.403746 GCTGCCTAAGTTAACTTCTCCAATTC 60.404 42.308 23.76 7.09 37.40 2.17
3195 3358 5.944007 TGCCTAAGTTAACTTCTCCAATTCC 59.056 40.000 23.76 5.07 37.40 3.01
3196 3359 6.181190 GCCTAAGTTAACTTCTCCAATTCCT 58.819 40.000 23.76 0.00 37.40 3.36
3197 3360 7.037873 TGCCTAAGTTAACTTCTCCAATTCCTA 60.038 37.037 23.76 1.79 37.40 2.94
3200 3363 6.954352 AGTTAACTTCTCCAATTCCTACCT 57.046 37.500 1.12 0.00 0.00 3.08
3202 3365 8.445361 AGTTAACTTCTCCAATTCCTACCTTA 57.555 34.615 1.12 0.00 0.00 2.69
3203 3366 8.319881 AGTTAACTTCTCCAATTCCTACCTTAC 58.680 37.037 1.12 0.00 0.00 2.34
3204 3367 6.954352 AACTTCTCCAATTCCTACCTTACT 57.046 37.500 0.00 0.00 0.00 2.24
3206 3369 7.331089 ACTTCTCCAATTCCTACCTTACTTT 57.669 36.000 0.00 0.00 0.00 2.66
3207 3370 7.395617 ACTTCTCCAATTCCTACCTTACTTTC 58.604 38.462 0.00 0.00 0.00 2.62
3208 3371 7.237887 ACTTCTCCAATTCCTACCTTACTTTCT 59.762 37.037 0.00 0.00 0.00 2.52
3209 3372 6.947464 TCTCCAATTCCTACCTTACTTTCTG 58.053 40.000 0.00 0.00 0.00 3.02
3226 3408 5.946377 ACTTTCTGTGTTCAGGAACTTCTTT 59.054 36.000 12.86 0.00 41.67 2.52
3238 3420 3.181454 GGAACTTCTTTGGTGACTGGAGA 60.181 47.826 0.00 0.00 0.00 3.71
3424 3609 0.603569 TCTCTGTGAAGAAGCCCGTC 59.396 55.000 0.00 0.00 0.00 4.79
3437 3622 3.767230 CCGTCGTTGCGCTCACAG 61.767 66.667 9.73 2.67 0.00 3.66
3438 3623 3.030308 CGTCGTTGCGCTCACAGT 61.030 61.111 9.73 0.00 0.00 3.55
3440 3625 2.355837 TCGTTGCGCTCACAGTCC 60.356 61.111 9.73 0.00 0.00 3.85
3441 3626 3.414700 CGTTGCGCTCACAGTCCC 61.415 66.667 9.73 0.00 0.00 4.46
3442 3627 2.280797 GTTGCGCTCACAGTCCCA 60.281 61.111 9.73 0.00 0.00 4.37
3443 3628 1.672356 GTTGCGCTCACAGTCCCAT 60.672 57.895 9.73 0.00 0.00 4.00
3483 3668 0.529337 AGTGCATCGATCCTTCAGCG 60.529 55.000 0.00 0.00 0.00 5.18
3512 3697 8.334263 TCTTTTGCATGATATTGTTGTAGACA 57.666 30.769 0.00 0.00 36.19 3.41
3574 3759 2.582052 TCGCACTTTTGTCCCAGATTT 58.418 42.857 0.00 0.00 0.00 2.17
3686 3874 0.532862 GGACAGGCGGTATGTGATGG 60.533 60.000 0.00 0.00 0.00 3.51
3687 3875 1.153168 ACAGGCGGTATGTGATGGC 60.153 57.895 0.00 0.00 0.00 4.40
3718 3906 2.739379 GTGCTGCACTAGGTTCTTCTTC 59.261 50.000 24.68 0.00 0.00 2.87
3719 3907 2.634940 TGCTGCACTAGGTTCTTCTTCT 59.365 45.455 0.00 0.00 0.00 2.85
3720 3908 3.071602 TGCTGCACTAGGTTCTTCTTCTT 59.928 43.478 0.00 0.00 0.00 2.52
3721 3909 3.682377 GCTGCACTAGGTTCTTCTTCTTC 59.318 47.826 0.00 0.00 0.00 2.87
3747 3935 3.597255 GTTCTTGGGCTGTAGGTACTTC 58.403 50.000 0.00 0.00 41.75 3.01
3748 3936 3.185880 TCTTGGGCTGTAGGTACTTCT 57.814 47.619 0.00 0.00 41.75 2.85
3771 4398 1.163554 GTCTCACCGACGACCTACTT 58.836 55.000 0.00 0.00 32.04 2.24
3772 4399 1.135746 GTCTCACCGACGACCTACTTG 60.136 57.143 0.00 0.00 32.04 3.16
3773 4400 1.162698 CTCACCGACGACCTACTTGA 58.837 55.000 0.00 0.00 0.00 3.02
3777 4416 0.242825 CCGACGACCTACTTGAAGCA 59.757 55.000 0.00 0.00 0.00 3.91
3851 4493 3.745975 CGCCAACTGAATCTTACAGAACA 59.254 43.478 0.00 0.00 38.55 3.18
3948 4618 3.638160 GGAGAAGAGTGAGCTCATCAGAT 59.362 47.826 21.47 5.69 44.00 2.90
3971 4641 4.462483 TGCAAAAGATGTCCCTTAATCCAC 59.538 41.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 171 3.763931 TGGAACAAACTGGGGATGG 57.236 52.632 0.00 0.00 31.92 3.51
457 460 4.081697 TCACTGTTCGATCTGCCTATTTGA 60.082 41.667 0.00 0.00 0.00 2.69
555 558 1.299468 CTATCTGCTCACCGACGCC 60.299 63.158 0.00 0.00 0.00 5.68
561 564 8.718102 TTACACTATTTTTCTATCTGCTCACC 57.282 34.615 0.00 0.00 0.00 4.02
587 591 2.508526 ACGAGCTGAAGCCAGATTTTT 58.491 42.857 0.00 0.00 43.02 1.94
639 643 4.484537 AGGTGATGTCAGAGGAGATTTG 57.515 45.455 0.00 0.00 0.00 2.32
660 672 0.657951 GGCGCTTGCGTTTTCGTTTA 60.658 50.000 16.38 0.00 46.03 2.01
677 689 0.249657 GTGATCGACAGGAGGATGGC 60.250 60.000 0.00 0.00 0.00 4.40
691 703 1.202143 GCGACAATTTTCGGGGTGATC 60.202 52.381 15.25 0.00 39.50 2.92
768 780 0.037734 GGAAAGCGGAGGAAAAGGGA 59.962 55.000 0.00 0.00 0.00 4.20
769 781 0.965866 GGGAAAGCGGAGGAAAAGGG 60.966 60.000 0.00 0.00 0.00 3.95
770 782 0.038310 AGGGAAAGCGGAGGAAAAGG 59.962 55.000 0.00 0.00 0.00 3.11
834 851 1.674651 GGGAGTGGGGTTTCTTCGC 60.675 63.158 0.00 0.00 0.00 4.70
839 856 1.597461 CGAGAGGGAGTGGGGTTTC 59.403 63.158 0.00 0.00 0.00 2.78
840 857 2.593956 GCGAGAGGGAGTGGGGTTT 61.594 63.158 0.00 0.00 0.00 3.27
841 858 3.003763 GCGAGAGGGAGTGGGGTT 61.004 66.667 0.00 0.00 0.00 4.11
842 859 3.966930 GAGCGAGAGGGAGTGGGGT 62.967 68.421 0.00 0.00 0.00 4.95
843 860 3.151022 GAGCGAGAGGGAGTGGGG 61.151 72.222 0.00 0.00 0.00 4.96
844 861 3.151022 GGAGCGAGAGGGAGTGGG 61.151 72.222 0.00 0.00 0.00 4.61
845 862 2.363018 TGGAGCGAGAGGGAGTGG 60.363 66.667 0.00 0.00 0.00 4.00
846 863 2.716017 GGTGGAGCGAGAGGGAGTG 61.716 68.421 0.00 0.00 0.00 3.51
847 864 2.363147 GGTGGAGCGAGAGGGAGT 60.363 66.667 0.00 0.00 0.00 3.85
848 865 3.522731 CGGTGGAGCGAGAGGGAG 61.523 72.222 0.00 0.00 0.00 4.30
851 868 3.827898 GTCCGGTGGAGCGAGAGG 61.828 72.222 0.00 0.00 29.39 3.69
852 869 4.180946 CGTCCGGTGGAGCGAGAG 62.181 72.222 0.00 0.00 31.51 3.20
871 888 4.711949 AACGGCTGGCTGCTCTGG 62.712 66.667 16.14 6.11 42.39 3.86
872 889 2.670934 AAACGGCTGGCTGCTCTG 60.671 61.111 16.14 8.92 42.39 3.35
873 890 2.359230 GAAACGGCTGGCTGCTCT 60.359 61.111 16.14 0.00 42.39 4.09
874 891 3.435186 GGAAACGGCTGGCTGCTC 61.435 66.667 16.14 5.63 42.39 4.26
875 892 3.574074 ATGGAAACGGCTGGCTGCT 62.574 57.895 16.14 0.00 42.39 4.24
876 893 3.056313 GATGGAAACGGCTGGCTGC 62.056 63.158 7.96 7.96 41.94 5.25
877 894 2.753966 CGATGGAAACGGCTGGCTG 61.754 63.158 0.00 0.00 0.00 4.85
878 895 2.436646 CGATGGAAACGGCTGGCT 60.437 61.111 0.00 0.00 0.00 4.75
879 896 4.179579 GCGATGGAAACGGCTGGC 62.180 66.667 0.00 0.00 30.42 4.85
888 905 1.103987 CCTCTCTCCTCGCGATGGAA 61.104 60.000 22.04 14.46 32.61 3.53
890 907 2.560119 CCCTCTCTCCTCGCGATGG 61.560 68.421 10.36 13.83 0.00 3.51
893 910 2.190843 CTCCCTCTCTCCTCGCGA 59.809 66.667 9.26 9.26 0.00 5.87
919 952 2.060980 GGGAGCGTGATCCTGGAGT 61.061 63.158 1.52 0.00 39.50 3.85
993 1026 4.950062 TCCTGATCCATCGCGCGC 62.950 66.667 27.95 23.91 0.00 6.86
1736 1790 3.460672 CTGGCACTCACCACACCGT 62.461 63.158 0.00 0.00 35.33 4.83
1797 1851 1.887707 GCCTAATTCCTGGGCGTCG 60.888 63.158 0.00 0.00 36.37 5.12
1808 1862 1.307517 TCGACCCCAGGGCCTAATT 60.308 57.895 5.28 0.00 39.32 1.40
1809 1863 1.766461 CTCGACCCCAGGGCCTAAT 60.766 63.158 5.28 0.00 39.32 1.73
1812 1866 4.658786 AACTCGACCCCAGGGCCT 62.659 66.667 0.00 0.00 39.32 5.19
1828 1882 3.309506 CAAATGCCGCCCCCACAA 61.310 61.111 0.00 0.00 0.00 3.33
2256 2310 1.021390 CAAGGAGCCGGTTGCAGTAG 61.021 60.000 13.20 0.00 44.83 2.57
2337 2391 3.482156 AGCATCTTGTCACTGAACACT 57.518 42.857 0.00 0.00 0.00 3.55
2373 2427 3.517296 TCAAGGGCCTTGACAATGTTA 57.483 42.857 38.53 18.83 44.27 2.41
2613 2667 2.774809 GGAGAACAAGATTAGGCCCTCT 59.225 50.000 0.00 0.00 0.00 3.69
3060 3178 1.341679 ACAGCAATGCCCTCATCACAT 60.342 47.619 0.00 0.00 31.27 3.21
3167 3314 3.685272 GGAGAAGTTAACTTAGGCAGCAC 59.315 47.826 20.58 6.12 36.11 4.40
3182 3345 6.954352 AAGTAAGGTAGGAATTGGAGAAGT 57.046 37.500 0.00 0.00 0.00 3.01
3188 3351 6.238648 ACACAGAAAGTAAGGTAGGAATTGG 58.761 40.000 0.00 0.00 0.00 3.16
3189 3352 7.444183 TGAACACAGAAAGTAAGGTAGGAATTG 59.556 37.037 0.00 0.00 0.00 2.32
3190 3353 7.514721 TGAACACAGAAAGTAAGGTAGGAATT 58.485 34.615 0.00 0.00 0.00 2.17
3191 3354 7.074653 TGAACACAGAAAGTAAGGTAGGAAT 57.925 36.000 0.00 0.00 0.00 3.01
3192 3355 6.463897 CCTGAACACAGAAAGTAAGGTAGGAA 60.464 42.308 0.00 0.00 33.94 3.36
3194 3357 5.011738 TCCTGAACACAGAAAGTAAGGTAGG 59.988 44.000 0.00 0.00 33.94 3.18
3195 3358 6.097915 TCCTGAACACAGAAAGTAAGGTAG 57.902 41.667 0.00 0.00 33.94 3.18
3196 3359 6.099269 AGTTCCTGAACACAGAAAGTAAGGTA 59.901 38.462 12.21 0.00 43.47 3.08
3197 3360 5.104485 AGTTCCTGAACACAGAAAGTAAGGT 60.104 40.000 12.21 0.00 43.47 3.50
3200 3363 6.650120 AGAAGTTCCTGAACACAGAAAGTAA 58.350 36.000 12.21 0.00 43.47 2.24
3202 3365 5.104259 AGAAGTTCCTGAACACAGAAAGT 57.896 39.130 12.21 0.00 43.47 2.66
3203 3366 6.261118 CAAAGAAGTTCCTGAACACAGAAAG 58.739 40.000 12.21 0.00 43.47 2.62
3204 3367 5.125417 CCAAAGAAGTTCCTGAACACAGAAA 59.875 40.000 12.21 0.00 43.47 2.52
3206 3369 4.199310 CCAAAGAAGTTCCTGAACACAGA 58.801 43.478 12.21 0.00 43.47 3.41
3207 3370 3.947834 ACCAAAGAAGTTCCTGAACACAG 59.052 43.478 12.21 0.00 43.47 3.66
3208 3371 3.694072 CACCAAAGAAGTTCCTGAACACA 59.306 43.478 12.21 0.00 43.47 3.72
3209 3372 3.945285 TCACCAAAGAAGTTCCTGAACAC 59.055 43.478 12.21 6.08 43.47 3.32
3226 3408 5.491070 CATTTAGATGTTCTCCAGTCACCA 58.509 41.667 0.00 0.00 0.00 4.17
3238 3420 2.164219 CACCGCAAGCCATTTAGATGTT 59.836 45.455 0.00 0.00 0.00 2.71
3420 3605 3.767230 CTGTGAGCGCAACGACGG 61.767 66.667 11.47 0.98 0.00 4.79
3424 3609 3.414700 GGGACTGTGAGCGCAACG 61.415 66.667 11.47 6.84 0.00 4.10
3435 3620 5.458041 ACACAATTTCTTTCATGGGACTG 57.542 39.130 0.00 0.00 0.00 3.51
3436 3621 7.451255 TGATTACACAATTTCTTTCATGGGACT 59.549 33.333 0.00 0.00 0.00 3.85
3437 3622 7.542130 GTGATTACACAATTTCTTTCATGGGAC 59.458 37.037 0.00 0.00 45.32 4.46
3438 3623 7.601856 GTGATTACACAATTTCTTTCATGGGA 58.398 34.615 0.00 0.00 45.32 4.37
3483 3668 7.656707 ACAACAATATCATGCAAAAGAAACC 57.343 32.000 0.00 0.00 0.00 3.27
3512 3697 7.868415 GCAAAGTTCCAGTCTATTCTACGATAT 59.132 37.037 0.00 0.00 0.00 1.63
3574 3759 2.500229 CTGGTTTCAGCTTAACCCGAA 58.500 47.619 19.81 1.98 43.55 4.30
3718 3906 3.356529 ACAGCCCAAGAACCATAGAAG 57.643 47.619 0.00 0.00 0.00 2.85
3719 3907 3.199946 CCTACAGCCCAAGAACCATAGAA 59.800 47.826 0.00 0.00 0.00 2.10
3720 3908 2.771943 CCTACAGCCCAAGAACCATAGA 59.228 50.000 0.00 0.00 0.00 1.98
3721 3909 2.505819 ACCTACAGCCCAAGAACCATAG 59.494 50.000 0.00 0.00 0.00 2.23
3771 4398 5.376625 ACTAACACCAGAATTTCTGCTTCA 58.623 37.500 19.04 4.02 42.98 3.02
3772 4399 5.948992 ACTAACACCAGAATTTCTGCTTC 57.051 39.130 19.04 0.00 42.98 3.86
3773 4400 9.515226 TTATTACTAACACCAGAATTTCTGCTT 57.485 29.630 19.04 12.19 42.98 3.91
3851 4493 4.392047 TGACAACATGTTCTGATGCTTCT 58.608 39.130 8.48 0.00 31.11 2.85
3948 4618 4.462483 GTGGATTAAGGGACATCTTTTGCA 59.538 41.667 0.00 0.00 0.00 4.08
3971 4641 6.598064 ACAAATTAAAACAGAGGAGGGATACG 59.402 38.462 0.00 0.00 37.60 3.06


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

AutoCloner maintained by Alex Coulton.