Multiple sequence alignment - TraesCS2A01G424400

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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 TraesCS2A01G424400 chr2A 100.000 4331 0 0 1 4331 678671872 678676202 0.000000e+00 7998.0
1 TraesCS2A01G424400 chr2A 78.818 406 48 23 3563 3948 164709775 164709388 5.600000e-59 239.0
2 TraesCS2A01G424400 chr2D 94.249 4121 137 36 1 4076 535572245 535576310 0.000000e+00 6205.0
3 TraesCS2A01G424400 chr2D 91.463 164 11 1 3959 4122 535576436 535576596 5.640000e-54 222.0
4 TraesCS2A01G424400 chr2D 96.850 127 4 0 4205 4331 535579158 535579284 3.390000e-51 213.0
5 TraesCS2A01G424400 chr2B 92.888 4176 193 53 1 4126 636776316 636780437 0.000000e+00 5971.0
6 TraesCS2A01G424400 chr2B 78.241 216 40 6 3735 3945 741212550 741212337 9.770000e-27 132.0
7 TraesCS2A01G424400 chr2B 93.506 77 3 2 4192 4267 636820249 636820324 3.540000e-21 113.0
8 TraesCS2A01G424400 chr7B 75.186 403 80 13 3563 3949 479873471 479873073 5.760000e-39 172.0
9 TraesCS2A01G424400 chr7B 75.186 403 80 13 3563 3949 479896682 479896284 5.760000e-39 172.0
10 TraesCS2A01G424400 chr3B 87.500 128 15 1 3735 3862 809044573 809044447 3.490000e-31 147.0
11 TraesCS2A01G424400 chr3D 79.695 197 31 7 3751 3942 374397453 374397645 2.720000e-27 134.0
12 TraesCS2A01G424400 chr1B 77.465 213 40 7 3735 3942 561301944 561301735 2.120000e-23 121.0
13 TraesCS2A01G424400 chr5A 87.719 57 7 0 3668 3724 378524133 378524077 2.800000e-07 67.6


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 TraesCS2A01G424400 chr2A 678671872 678676202 4330 False 7998.000000 7998 100.000000 1 4331 1 chr2A.!!$F1 4330
1 TraesCS2A01G424400 chr2D 535572245 535579284 7039 False 2213.333333 6205 94.187333 1 4331 3 chr2D.!!$F1 4330
2 TraesCS2A01G424400 chr2B 636776316 636780437 4121 False 5971.000000 5971 92.888000 1 4126 1 chr2B.!!$F1 4125

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
272 286 0.035458 AGCTGCCTACAACTGTGACC 59.965 55.0 0.00 0.0 0.00 4.02 F
451 467 0.179045 ACTGATTCATAGGCACGGGC 60.179 55.0 0.00 0.0 40.13 6.13 F
830 881 0.179936 GCAGGAGTAGCAGCCAAGAT 59.820 55.0 0.00 0.0 0.00 2.40 F
1806 1859 0.537143 TTGCACGTGCTGGAAGGATT 60.537 50.0 37.59 0.0 35.94 3.01 F
2893 2946 1.251527 ACGATGCGTCTGGAAGGTCT 61.252 55.0 4.05 0.0 33.69 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1481 1.118356 AGGACAGATCATCGGAGGGC 61.118 60.000 0.00 0.0 0.00 5.19 R
1437 1490 1.134699 GCCACGATGAAGGACAGATCA 60.135 52.381 0.00 0.0 0.00 2.92 R
2121 2174 2.437359 GCAGCGACATCCAGCCTT 60.437 61.111 0.00 0.0 0.00 4.35 R
2988 3041 0.318699 GCGTGTGCACTGTAGAGACA 60.319 55.000 19.41 0.0 42.15 3.41 R
3831 3903 0.670854 GGGAAAGACGACTGAGTGCC 60.671 60.000 0.00 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
124 125 0.901827 TGCCGACATTGCTTCTCCTA 59.098 50.000 0.00 0.00 0.00 2.94
183 189 2.159787 CGTGAGCTCAATGCACAGTTAC 60.160 50.000 20.19 0.00 42.56 2.50
257 263 3.561310 TCTTAGACAAGCAAACACAGCTG 59.439 43.478 13.48 13.48 42.53 4.24
258 264 0.383231 AGACAAGCAAACACAGCTGC 59.617 50.000 15.27 0.00 42.53 5.25
272 286 0.035458 AGCTGCCTACAACTGTGACC 59.965 55.000 0.00 0.00 0.00 4.02
280 294 1.037493 ACAACTGTGACCTCGCTACA 58.963 50.000 0.00 0.00 0.00 2.74
291 305 1.550065 CTCGCTACACAATCTGACCG 58.450 55.000 0.00 0.00 0.00 4.79
335 349 5.873712 ACTCAGAATTTCAGAGTGCTGTATG 59.126 40.000 19.92 0.00 40.94 2.39
336 350 5.798132 TCAGAATTTCAGAGTGCTGTATGT 58.202 37.500 0.00 0.00 42.84 2.29
337 351 5.640783 TCAGAATTTCAGAGTGCTGTATGTG 59.359 40.000 0.00 0.00 42.84 3.21
338 352 5.640783 CAGAATTTCAGAGTGCTGTATGTGA 59.359 40.000 0.00 0.00 42.84 3.58
339 353 5.873712 AGAATTTCAGAGTGCTGTATGTGAG 59.126 40.000 0.00 0.00 42.84 3.51
340 354 4.871933 TTTCAGAGTGCTGTATGTGAGA 57.128 40.909 0.00 0.00 42.84 3.27
420 436 1.338674 TGACAGGATAAACGCCCACTG 60.339 52.381 0.00 0.00 0.00 3.66
426 442 2.137177 ATAAACGCCCACTGCCCACT 62.137 55.000 0.00 0.00 36.24 4.00
451 467 0.179045 ACTGATTCATAGGCACGGGC 60.179 55.000 0.00 0.00 40.13 6.13
481 497 0.291989 CTGAACGAAATCGAGCGTCG 59.708 55.000 10.16 11.34 43.02 5.12
518 534 3.073650 ACCACAGAAAAGCTCTCCAATCT 59.926 43.478 0.00 0.00 29.07 2.40
527 543 2.504996 AGCTCTCCAATCTCTTCCCAAG 59.495 50.000 0.00 0.00 0.00 3.61
612 647 5.751028 GGACTCGAATCAATCAACCTAGAAG 59.249 44.000 0.00 0.00 0.00 2.85
685 720 4.813697 GCCAAACAACACCAAATTACACAT 59.186 37.500 0.00 0.00 0.00 3.21
706 741 1.149401 GCAGGGGATGGAGCTTACC 59.851 63.158 0.00 0.00 0.00 2.85
737 772 3.373565 CGAAGCAAACAGGGGGCC 61.374 66.667 0.00 0.00 0.00 5.80
738 773 3.373565 GAAGCAAACAGGGGGCCG 61.374 66.667 0.00 0.00 0.00 6.13
742 777 2.917227 CAAACAGGGGGCCGCTTT 60.917 61.111 22.03 12.58 0.00 3.51
786 837 2.041265 AGGGGGCGATCTGGTTCT 59.959 61.111 0.00 0.00 0.00 3.01
787 838 2.190578 GGGGGCGATCTGGTTCTG 59.809 66.667 0.00 0.00 0.00 3.02
812 863 0.973496 AGAGGAAGACGAAGGGAGGC 60.973 60.000 0.00 0.00 0.00 4.70
830 881 0.179936 GCAGGAGTAGCAGCCAAGAT 59.820 55.000 0.00 0.00 0.00 2.40
852 904 4.862823 CGGGAGGAGGAGGGGGAC 62.863 77.778 0.00 0.00 0.00 4.46
858 910 2.764128 GAGGAGGGGGACGATGCA 60.764 66.667 0.00 0.00 0.00 3.96
889 941 2.034685 CGAGATTTAGATGGCTCGGTCA 59.965 50.000 0.00 0.00 44.58 4.02
893 945 3.627395 TTTAGATGGCTCGGTCATGTT 57.373 42.857 0.00 0.00 0.00 2.71
894 946 3.627395 TTAGATGGCTCGGTCATGTTT 57.373 42.857 0.00 0.00 0.00 2.83
895 947 1.742761 AGATGGCTCGGTCATGTTTG 58.257 50.000 0.00 0.00 0.00 2.93
896 948 0.734889 GATGGCTCGGTCATGTTTGG 59.265 55.000 0.00 0.00 0.00 3.28
897 949 0.680921 ATGGCTCGGTCATGTTTGGG 60.681 55.000 0.00 0.00 0.00 4.12
898 950 2.700773 GGCTCGGTCATGTTTGGGC 61.701 63.158 0.00 0.00 0.00 5.36
899 951 2.700773 GCTCGGTCATGTTTGGGCC 61.701 63.158 0.00 0.00 0.00 5.80
900 952 2.359354 TCGGTCATGTTTGGGCCG 60.359 61.111 0.00 0.00 40.58 6.13
901 953 2.671619 CGGTCATGTTTGGGCCGT 60.672 61.111 0.00 0.00 37.18 5.68
902 954 2.961768 GGTCATGTTTGGGCCGTG 59.038 61.111 0.00 0.00 0.00 4.94
903 955 1.901464 GGTCATGTTTGGGCCGTGT 60.901 57.895 0.00 0.00 0.00 4.49
978 1031 2.498726 CCGAGAAGGGCTGAGAGC 59.501 66.667 0.00 0.00 41.46 4.09
988 1041 3.189568 GCTGAGAGCCTGAGAGAGA 57.810 57.895 0.00 0.00 34.48 3.10
989 1042 0.740737 GCTGAGAGCCTGAGAGAGAC 59.259 60.000 0.00 0.00 34.48 3.36
990 1043 1.392589 CTGAGAGCCTGAGAGAGACC 58.607 60.000 0.00 0.00 0.00 3.85
991 1044 0.701147 TGAGAGCCTGAGAGAGACCA 59.299 55.000 0.00 0.00 0.00 4.02
992 1045 1.102978 GAGAGCCTGAGAGAGACCAC 58.897 60.000 0.00 0.00 0.00 4.16
993 1046 0.679640 AGAGCCTGAGAGAGACCACG 60.680 60.000 0.00 0.00 0.00 4.94
994 1047 2.183046 GCCTGAGAGAGACCACGC 59.817 66.667 0.00 0.00 0.00 5.34
1119 1172 2.460918 GTCGAATGGATAGACACGGTG 58.539 52.381 6.58 6.58 35.19 4.94
1437 1490 3.000819 TGGTTCGTGCCCTCCGAT 61.001 61.111 0.00 0.00 33.81 4.18
1806 1859 0.537143 TTGCACGTGCTGGAAGGATT 60.537 50.000 37.59 0.00 35.94 3.01
1851 1904 2.507058 TGAAATGAGACAGAGGGATGGG 59.493 50.000 0.00 0.00 0.00 4.00
2121 2174 1.971167 GGCAAATGCACGGTCAGGA 60.971 57.895 7.80 0.00 44.36 3.86
2478 2531 1.675641 GCGGTTCATGGGTTCTGCT 60.676 57.895 0.00 0.00 0.00 4.24
2893 2946 1.251527 ACGATGCGTCTGGAAGGTCT 61.252 55.000 4.05 0.00 33.69 3.85
2943 2996 2.665649 TCGTATTCGACCAGCACATT 57.334 45.000 0.00 0.00 41.35 2.71
2994 3047 4.443266 GGAGCGGCGCTTGTCTCT 62.443 66.667 36.73 12.30 39.88 3.10
3538 3591 4.095782 AGTGTGACGTGTTGCACTTATTTT 59.904 37.500 0.00 0.00 38.86 1.82
3539 3592 4.796312 GTGTGACGTGTTGCACTTATTTTT 59.204 37.500 0.00 0.00 36.05 1.94
3581 3634 5.913137 TTCGAATATCCAATTTTGTGCCT 57.087 34.783 0.00 0.00 0.00 4.75
3679 3744 0.108615 GAGTATGTGAGGTGCGTGCT 60.109 55.000 0.00 0.00 0.00 4.40
3831 3903 2.228582 TGAAATTTGGCACGGACATCAG 59.771 45.455 0.00 0.00 0.00 2.90
3913 3986 7.843490 TTCTAACGATTTTTATCACTCCCTG 57.157 36.000 0.00 0.00 0.00 4.45
3994 4067 6.598525 TGAAGAACAGTTGTTACATATTGCG 58.401 36.000 0.00 0.00 38.56 4.85
4003 4076 8.436970 CAGTTGTTACATATTGCGTTGTTACTA 58.563 33.333 0.00 0.00 0.00 1.82
4026 4219 4.012374 TCTCAGAAAATCCATTCCAGTGC 58.988 43.478 0.00 0.00 0.00 4.40
4043 4236 7.786178 TCCAGTGCACTTCAATAACATATAC 57.214 36.000 18.94 0.00 0.00 1.47
4145 4458 7.693969 AAAAAGAGAGAGAGAGAAGAGAGAG 57.306 40.000 0.00 0.00 0.00 3.20
4146 4459 6.627087 AAAGAGAGAGAGAGAAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
4147 4460 5.867903 AGAGAGAGAGAGAAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
4148 4461 5.523588 AGAGAGAGAGAGAAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
4149 4462 5.598005 AGAGAGAGAGAGAAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
4150 4463 5.523588 AGAGAGAGAGAAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
4151 4464 5.598005 AGAGAGAGAGAAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
4152 4465 5.523588 AGAGAGAGAAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
4153 4466 5.598005 AGAGAGAGAAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
4154 4467 5.523588 AGAGAGAAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
4155 4468 5.598005 AGAGAGAAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
4156 4469 5.523588 AGAGAAGAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
4157 4470 5.598005 AGAGAAGAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
4173 4486 9.469097 GAGAGAGAGAGAGAGATAGAGTACTAT 57.531 40.741 0.00 0.00 41.41 2.12
4174 4487 9.249053 AGAGAGAGAGAGAGATAGAGTACTATG 57.751 40.741 0.00 0.00 39.16 2.23
4175 4488 8.958060 AGAGAGAGAGAGATAGAGTACTATGT 57.042 38.462 0.00 0.00 39.16 2.29
4176 4489 9.381038 AGAGAGAGAGAGATAGAGTACTATGTT 57.619 37.037 0.00 0.00 39.16 2.71
4177 4490 9.998106 GAGAGAGAGAGATAGAGTACTATGTTT 57.002 37.037 0.00 0.00 39.16 2.83
4232 7050 1.079405 GCGATGTGAACGAAGGGGA 60.079 57.895 0.00 0.00 0.00 4.81
4236 7054 2.095919 CGATGTGAACGAAGGGGAAAAC 60.096 50.000 0.00 0.00 0.00 2.43
4262 7080 2.269520 ATTGCAGGCCCATGTAGCGA 62.270 55.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.101650 ACCAGATTTTTCCAGGTTTGATTC 57.898 37.500 0.00 0.00 0.00 2.52
124 125 4.470664 TGCCTTTTTATCAGCATTCCCATT 59.529 37.500 0.00 0.00 0.00 3.16
257 263 1.014564 GCGAGGTCACAGTTGTAGGC 61.015 60.000 0.00 0.00 0.00 3.93
258 264 0.603569 AGCGAGGTCACAGTTGTAGG 59.396 55.000 0.00 0.00 0.00 3.18
272 286 1.550065 CGGTCAGATTGTGTAGCGAG 58.450 55.000 0.00 0.00 34.99 5.03
280 294 1.192428 GGTAGGTCCGGTCAGATTGT 58.808 55.000 0.00 0.00 0.00 2.71
291 305 0.252558 TTGGGTGGAGAGGTAGGTCC 60.253 60.000 0.00 0.00 0.00 4.46
335 349 6.770785 AGATAAGTATGGAGTCTCAGTCTCAC 59.229 42.308 1.47 0.00 34.04 3.51
336 350 6.905736 AGATAAGTATGGAGTCTCAGTCTCA 58.094 40.000 1.47 0.00 34.04 3.27
337 351 8.154856 AGTAGATAAGTATGGAGTCTCAGTCTC 58.845 40.741 1.47 0.00 0.00 3.36
338 352 8.041143 AGTAGATAAGTATGGAGTCTCAGTCT 57.959 38.462 1.47 0.00 0.00 3.24
339 353 8.685838 AAGTAGATAAGTATGGAGTCTCAGTC 57.314 38.462 1.47 0.00 0.00 3.51
340 354 8.499406 AGAAGTAGATAAGTATGGAGTCTCAGT 58.501 37.037 1.47 0.00 0.00 3.41
420 436 1.078426 AATCAGTACGGCAGTGGGC 60.078 57.895 0.00 0.00 43.74 5.36
426 442 1.760029 TGCCTATGAATCAGTACGGCA 59.240 47.619 11.64 11.64 43.12 5.69
451 467 5.059660 GATTTCGTTCAGTAATCGCTCTG 57.940 43.478 0.00 0.00 29.26 3.35
518 534 6.462347 GCTGTTAAATTTTGGTCTTGGGAAGA 60.462 38.462 0.00 0.00 34.51 2.87
527 543 5.014202 TCCCTAGGCTGTTAAATTTTGGTC 58.986 41.667 2.05 0.00 0.00 4.02
554 580 7.798596 TGATTGGTAGTAGTAGCAGTAGTAC 57.201 40.000 9.31 0.00 37.92 2.73
562 588 9.632807 CTTGATTAGATGATTGGTAGTAGTAGC 57.367 37.037 0.00 0.00 0.00 3.58
612 647 4.054671 CGAGATGGAATTAGGCTCTGTTC 58.945 47.826 0.00 0.00 0.00 3.18
685 720 2.856208 TAAGCTCCATCCCCTGCCCA 62.856 60.000 0.00 0.00 0.00 5.36
706 741 2.125552 TTCGCGGCACCAGATCAG 60.126 61.111 6.13 0.00 0.00 2.90
734 769 3.577313 GATCGGAGCAAAGCGGCC 61.577 66.667 0.00 0.00 0.00 6.13
737 772 1.153568 TCCAGATCGGAGCAAAGCG 60.154 57.895 0.00 0.00 39.64 4.68
738 773 4.941609 TCCAGATCGGAGCAAAGC 57.058 55.556 0.00 0.00 39.64 3.51
745 780 4.458829 ACCCGCCTCCAGATCGGA 62.459 66.667 9.28 6.21 45.53 4.55
786 837 0.541998 TTCGTCTTCCTCTGCCTCCA 60.542 55.000 0.00 0.00 0.00 3.86
787 838 0.174617 CTTCGTCTTCCTCTGCCTCC 59.825 60.000 0.00 0.00 0.00 4.30
812 863 1.950828 CATCTTGGCTGCTACTCCTG 58.049 55.000 0.00 0.00 0.00 3.86
825 876 1.153289 CTCCTCCCGTGGCATCTTG 60.153 63.158 0.00 0.00 0.00 3.02
852 904 0.028505 CTCGAGCCCAAAATGCATCG 59.971 55.000 0.00 0.00 33.62 3.84
858 910 4.823989 CCATCTAAATCTCGAGCCCAAAAT 59.176 41.667 7.81 0.00 0.00 1.82
889 941 0.323360 AGCATACACGGCCCAAACAT 60.323 50.000 0.00 0.00 0.00 2.71
893 945 2.125310 CGAGCATACACGGCCCAA 60.125 61.111 0.00 0.00 0.00 4.12
894 946 2.949909 AACGAGCATACACGGCCCA 61.950 57.895 0.00 0.00 33.86 5.36
895 947 2.125269 AACGAGCATACACGGCCC 60.125 61.111 0.00 0.00 33.86 5.80
896 948 1.447140 TCAACGAGCATACACGGCC 60.447 57.895 0.00 0.00 33.86 6.13
897 949 1.708027 GTCAACGAGCATACACGGC 59.292 57.895 0.00 0.00 33.86 5.68
898 950 0.731514 ACGTCAACGAGCATACACGG 60.732 55.000 9.88 0.00 43.02 4.94
899 951 1.057636 AACGTCAACGAGCATACACG 58.942 50.000 9.88 0.00 43.02 4.49
900 952 1.126113 CCAACGTCAACGAGCATACAC 59.874 52.381 9.88 0.00 43.02 2.90
901 953 1.424403 CCAACGTCAACGAGCATACA 58.576 50.000 9.88 0.00 43.02 2.29
902 954 0.719465 CCCAACGTCAACGAGCATAC 59.281 55.000 9.88 0.00 43.02 2.39
903 955 1.017177 GCCCAACGTCAACGAGCATA 61.017 55.000 9.88 0.00 43.02 3.14
978 1031 1.943116 CTGGCGTGGTCTCTCTCAGG 61.943 65.000 0.00 0.00 0.00 3.86
979 1032 0.962855 TCTGGCGTGGTCTCTCTCAG 60.963 60.000 0.00 0.00 0.00 3.35
980 1033 0.323816 ATCTGGCGTGGTCTCTCTCA 60.324 55.000 0.00 0.00 0.00 3.27
981 1034 1.681538 TATCTGGCGTGGTCTCTCTC 58.318 55.000 0.00 0.00 0.00 3.20
982 1035 1.959985 CATATCTGGCGTGGTCTCTCT 59.040 52.381 0.00 0.00 0.00 3.10
983 1036 1.604185 GCATATCTGGCGTGGTCTCTC 60.604 57.143 0.00 0.00 0.00 3.20
984 1037 0.390860 GCATATCTGGCGTGGTCTCT 59.609 55.000 0.00 0.00 0.00 3.10
986 1039 0.390860 GAGCATATCTGGCGTGGTCT 59.609 55.000 0.00 0.00 37.39 3.85
987 1040 0.601311 GGAGCATATCTGGCGTGGTC 60.601 60.000 0.00 0.00 39.08 4.02
988 1041 1.050988 AGGAGCATATCTGGCGTGGT 61.051 55.000 0.00 0.00 36.08 4.16
989 1042 0.320247 GAGGAGCATATCTGGCGTGG 60.320 60.000 0.00 0.00 36.08 4.94
990 1043 0.320247 GGAGGAGCATATCTGGCGTG 60.320 60.000 0.00 0.00 36.08 5.34
991 1044 1.810606 CGGAGGAGCATATCTGGCGT 61.811 60.000 0.00 0.00 36.08 5.68
992 1045 1.080230 CGGAGGAGCATATCTGGCG 60.080 63.158 0.00 0.00 36.08 5.69
993 1046 1.375268 GCGGAGGAGCATATCTGGC 60.375 63.158 0.00 0.00 37.05 4.85
994 1047 1.080230 CGCGGAGGAGCATATCTGG 60.080 63.158 0.00 0.00 36.85 3.86
1119 1172 1.375098 CCGTCTCGTCCAGGTAGTCC 61.375 65.000 0.00 0.00 0.00 3.85
1428 1481 1.118356 AGGACAGATCATCGGAGGGC 61.118 60.000 0.00 0.00 0.00 5.19
1437 1490 1.134699 GCCACGATGAAGGACAGATCA 60.135 52.381 0.00 0.00 0.00 2.92
1725 1778 3.039202 GCCCGCCACAGACATTTCG 62.039 63.158 0.00 0.00 0.00 3.46
2121 2174 2.437359 GCAGCGACATCCAGCCTT 60.437 61.111 0.00 0.00 0.00 4.35
2478 2531 4.399219 TGAAATTGTTGGTTCGTATCCCA 58.601 39.130 0.00 0.00 0.00 4.37
2908 2961 0.541863 ACGATGGCCTTAGGGAACAG 59.458 55.000 3.32 0.00 33.58 3.16
2943 2996 2.204136 ATGTCCAGGGACCAGGCA 60.204 61.111 15.53 0.00 43.97 4.75
2988 3041 0.318699 GCGTGTGCACTGTAGAGACA 60.319 55.000 19.41 0.00 42.15 3.41
3538 3591 6.826231 TCGAAAAATCCTCAACTATATGCCAA 59.174 34.615 0.00 0.00 0.00 4.52
3539 3592 6.353323 TCGAAAAATCCTCAACTATATGCCA 58.647 36.000 0.00 0.00 0.00 4.92
3581 3634 1.764723 CACTGGATGTAGATGAGCCCA 59.235 52.381 0.00 0.00 0.00 5.36
3646 3711 8.489489 ACCTCACATACTCAATCATCTTACATT 58.511 33.333 0.00 0.00 0.00 2.71
3664 3729 2.113860 ATTTAGCACGCACCTCACAT 57.886 45.000 0.00 0.00 0.00 3.21
3725 3791 2.948979 CACTGTTTGTGCAGACCCTTTA 59.051 45.455 0.00 0.00 40.06 1.85
3831 3903 0.670854 GGGAAAGACGACTGAGTGCC 60.671 60.000 0.00 0.00 0.00 5.01
3887 3960 8.175716 CAGGGAGTGATAAAAATCGTTAGAAAC 58.824 37.037 0.00 0.00 0.00 2.78
3891 3964 5.007724 GCCAGGGAGTGATAAAAATCGTTAG 59.992 44.000 0.00 0.00 0.00 2.34
3895 3968 3.545703 AGCCAGGGAGTGATAAAAATCG 58.454 45.455 0.00 0.00 0.00 3.34
3903 3976 1.129917 CATCTGAGCCAGGGAGTGAT 58.870 55.000 2.86 0.00 31.51 3.06
3980 4053 9.373603 AGATAGTAACAACGCAATATGTAACAA 57.626 29.630 0.00 0.00 0.00 2.83
3990 4063 7.148474 GGATTTTCTGAGATAGTAACAACGCAA 60.148 37.037 0.00 0.00 0.00 4.85
4003 4076 4.643784 GCACTGGAATGGATTTTCTGAGAT 59.356 41.667 0.00 0.00 0.00 2.75
4026 4219 5.758296 ACCCTGCGTATATGTTATTGAAGTG 59.242 40.000 0.00 0.00 0.00 3.16
4043 4236 1.953559 ATGTATTGCTGTACCCTGCG 58.046 50.000 0.00 0.00 38.28 5.18
4126 4439 5.596361 TCTCTCTCTCTCTTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
4128 4441 5.596361 TCTCTCTCTCTCTCTTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
4130 4443 5.596361 TCTCTCTCTCTCTCTCTTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
4132 4445 5.596361 TCTCTCTCTCTCTCTCTCTTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
4133 4446 5.523588 TCTCTCTCTCTCTCTCTCTTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
4134 4447 5.596361 TCTCTCTCTCTCTCTCTCTCTTCTC 59.404 48.000 0.00 0.00 0.00 2.87
4135 4448 5.523588 TCTCTCTCTCTCTCTCTCTCTTCT 58.476 45.833 0.00 0.00 0.00 2.85
4136 4449 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
4137 4450 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
4138 4451 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4139 4452 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4140 4453 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
4141 4454 6.945435 TCTATCTCTCTCTCTCTCTCTCTCTC 59.055 46.154 0.00 0.00 0.00 3.20
4142 4455 6.857848 TCTATCTCTCTCTCTCTCTCTCTCT 58.142 44.000 0.00 0.00 0.00 3.10
4143 4456 6.719370 ACTCTATCTCTCTCTCTCTCTCTCTC 59.281 46.154 0.00 0.00 0.00 3.20
4144 4457 6.619464 ACTCTATCTCTCTCTCTCTCTCTCT 58.381 44.000 0.00 0.00 0.00 3.10
4145 4458 6.909550 ACTCTATCTCTCTCTCTCTCTCTC 57.090 45.833 0.00 0.00 0.00 3.20
4146 4459 7.531317 AGTACTCTATCTCTCTCTCTCTCTCT 58.469 42.308 0.00 0.00 0.00 3.10
4147 4460 7.768807 AGTACTCTATCTCTCTCTCTCTCTC 57.231 44.000 0.00 0.00 0.00 3.20
4148 4461 9.249053 CATAGTACTCTATCTCTCTCTCTCTCT 57.751 40.741 0.00 0.00 34.98 3.10
4149 4462 9.026121 ACATAGTACTCTATCTCTCTCTCTCTC 57.974 40.741 0.00 0.00 34.98 3.20
4150 4463 8.958060 ACATAGTACTCTATCTCTCTCTCTCT 57.042 38.462 0.00 0.00 34.98 3.10
4151 4464 9.998106 AAACATAGTACTCTATCTCTCTCTCTC 57.002 37.037 0.00 0.00 34.98 3.20
4181 4494 9.569167 CATAGTACTCTATCGTTGTCTCAAAAA 57.431 33.333 0.00 0.00 34.98 1.94
4183 4496 8.182227 CACATAGTACTCTATCGTTGTCTCAAA 58.818 37.037 0.00 0.00 34.98 2.69
4184 4497 7.551617 TCACATAGTACTCTATCGTTGTCTCAA 59.448 37.037 0.00 0.00 34.98 3.02
4185 4498 7.046033 TCACATAGTACTCTATCGTTGTCTCA 58.954 38.462 0.00 0.00 34.98 3.27
4188 4501 9.814507 CTTATCACATAGTACTCTATCGTTGTC 57.185 37.037 0.00 0.00 34.98 3.18
4190 4503 7.478978 CGCTTATCACATAGTACTCTATCGTTG 59.521 40.741 0.00 0.00 34.98 4.10
4192 4505 6.872547 TCGCTTATCACATAGTACTCTATCGT 59.127 38.462 0.00 0.00 34.98 3.73
4193 4506 7.292129 TCGCTTATCACATAGTACTCTATCG 57.708 40.000 0.00 0.00 34.98 2.92
4194 4507 8.670135 ACATCGCTTATCACATAGTACTCTATC 58.330 37.037 0.00 0.00 34.98 2.08
4195 4508 8.454894 CACATCGCTTATCACATAGTACTCTAT 58.545 37.037 0.00 0.00 37.35 1.98
4197 4510 6.486993 TCACATCGCTTATCACATAGTACTCT 59.513 38.462 0.00 0.00 0.00 3.24
4199 4512 6.635030 TCACATCGCTTATCACATAGTACT 57.365 37.500 0.00 0.00 0.00 2.73
4201 4514 5.912955 CGTTCACATCGCTTATCACATAGTA 59.087 40.000 0.00 0.00 0.00 1.82
4203 4516 4.976116 TCGTTCACATCGCTTATCACATAG 59.024 41.667 0.00 0.00 0.00 2.23
4232 7050 2.635443 CCTGCAATCGGCCCGTTTT 61.635 57.895 1.63 0.00 43.89 2.43


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

AutoCloner maintained by Alex Coulton.