Multiple sequence alignment - TraesCS5B01G533000

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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 TraesCS5B01G533000 chr5B 100.000 4596 0 0 1 4596 690089753 690094348 0.000000e+00 8488.0
1 TraesCS5B01G533000 chr5B 87.097 217 26 2 4381 4596 576252376 576252161 1.280000e-60 244.0
2 TraesCS5B01G533000 chr5D 93.382 4654 190 68 1 4596 546917705 546922298 0.000000e+00 6780.0
3 TraesCS5B01G533000 chr5D 88.961 462 37 10 1836 2297 388394936 388394489 4.020000e-155 558.0
4 TraesCS5B01G533000 chr5D 88.110 471 42 10 1827 2297 462802523 462802979 8.690000e-152 547.0
5 TraesCS5B01G533000 chr4A 91.197 2681 155 35 1 2665 621820129 621817514 0.000000e+00 3568.0
6 TraesCS5B01G533000 chr4A 93.457 1880 83 21 2746 4596 621817512 621815644 0.000000e+00 2754.0
7 TraesCS5B01G533000 chr1B 88.528 462 39 9 1836 2297 629472368 629471921 8.690000e-152 547.0
8 TraesCS5B01G533000 chr3D 85.350 471 42 16 1827 2297 22231091 22231534 3.240000e-126 462.0
9 TraesCS5B01G533000 chr4B 88.079 302 22 10 1996 2297 626627893 626627606 3.400000e-91 346.0
10 TraesCS5B01G533000 chr5A 79.215 433 62 20 4184 4596 589384131 589383707 4.530000e-70 276.0
11 TraesCS5B01G533000 chr7D 93.750 64 4 0 2665 2728 611816959 611816896 3.780000e-16 97.1
12 TraesCS5B01G533000 chr7D 90.411 73 6 1 2661 2733 87769815 87769886 1.360000e-15 95.3
13 TraesCS5B01G533000 chr7D 87.838 74 9 0 2661 2734 165657857 165657930 2.280000e-13 87.9
14 TraesCS5B01G533000 chrUn 88.462 78 9 0 2662 2739 35292109 35292032 1.360000e-15 95.3
15 TraesCS5B01G533000 chrUn 88.462 78 9 0 2662 2739 319858024 319858101 1.360000e-15 95.3
16 TraesCS5B01G533000 chrUn 88.462 78 9 0 2662 2739 331092118 331092041 1.360000e-15 95.3
17 TraesCS5B01G533000 chr3A 87.179 78 10 0 2662 2739 10690880 10690957 6.330000e-14 89.8
18 TraesCS5B01G533000 chr2D 83.529 85 14 0 2655 2739 125724864 125724948 3.810000e-11 80.5


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 TraesCS5B01G533000 chr5B 690089753 690094348 4595 False 8488 8488 100.000 1 4596 1 chr5B.!!$F1 4595
1 TraesCS5B01G533000 chr5D 546917705 546922298 4593 False 6780 6780 93.382 1 4596 1 chr5D.!!$F2 4595
2 TraesCS5B01G533000 chr4A 621815644 621820129 4485 True 3161 3568 92.327 1 4596 2 chr4A.!!$R1 4595

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
624 663 0.107116 ACTCTAGATGCCGTCGGACT 60.107 55.0 17.49 12.84 0.00 3.85 F
625 664 0.309302 CTCTAGATGCCGTCGGACTG 59.691 60.0 17.49 0.39 0.00 3.51 F
967 1007 0.317479 AGCTTAGTTCAGCGTCGGTT 59.683 50.0 0.00 0.00 45.24 4.44 F
1936 1976 0.381801 ACTTCACAAGCCAAAGTGCG 59.618 50.0 0.00 0.00 35.76 5.34 F
3250 3301 0.820226 TCCAGGTTGCTGAGAGATCG 59.180 55.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1588 0.110056 CAATCTGCAAGTGCGACCAC 60.110 55.000 0.00 0.0 45.83 4.16 R
1903 1943 0.322456 TGAAGTGGAATCAAGGCCCG 60.322 55.000 0.00 0.0 0.00 6.13 R
2950 2999 1.156736 CCCACACGAAACAGACATCC 58.843 55.000 0.00 0.0 0.00 3.51 R
3481 3532 0.886563 ATGTGGCTTCTTGCTTCAGC 59.113 50.000 0.00 0.0 42.39 4.26 R
4343 4404 1.227943 GCAGCAGTCTTGTGGTGGA 60.228 57.895 5.31 0.0 44.49 4.02 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
20 21 2.593134 GCCTAGCATCGCGCAAGAG 61.593 63.158 8.75 0.00 46.13 2.85
75 77 1.414378 GCCCACGGATTTGTTTTTCG 58.586 50.000 0.00 0.00 0.00 3.46
164 167 3.977427 ACAAACTCCGCCATTTCTTTTC 58.023 40.909 0.00 0.00 0.00 2.29
165 168 3.636764 ACAAACTCCGCCATTTCTTTTCT 59.363 39.130 0.00 0.00 0.00 2.52
166 169 4.099419 ACAAACTCCGCCATTTCTTTTCTT 59.901 37.500 0.00 0.00 0.00 2.52
167 170 4.937201 AACTCCGCCATTTCTTTTCTTT 57.063 36.364 0.00 0.00 0.00 2.52
168 171 4.937201 ACTCCGCCATTTCTTTTCTTTT 57.063 36.364 0.00 0.00 0.00 2.27
170 173 3.389221 TCCGCCATTTCTTTTCTTTTGC 58.611 40.909 0.00 0.00 0.00 3.68
171 174 2.155539 CCGCCATTTCTTTTCTTTTGCG 59.844 45.455 0.00 0.00 39.23 4.85
172 175 2.155539 CGCCATTTCTTTTCTTTTGCGG 59.844 45.455 0.00 0.00 36.18 5.69
173 176 3.389221 GCCATTTCTTTTCTTTTGCGGA 58.611 40.909 0.00 0.00 0.00 5.54
174 177 3.429881 GCCATTTCTTTTCTTTTGCGGAG 59.570 43.478 0.00 0.00 0.00 4.63
175 178 3.989817 CCATTTCTTTTCTTTTGCGGAGG 59.010 43.478 0.00 0.00 0.00 4.30
176 179 4.261994 CCATTTCTTTTCTTTTGCGGAGGA 60.262 41.667 0.00 0.00 0.00 3.71
177 180 4.993029 TTTCTTTTCTTTTGCGGAGGAA 57.007 36.364 0.00 0.00 34.77 3.36
195 198 2.231478 GGAAAAGAAAAGTAGCCCAGCC 59.769 50.000 0.00 0.00 0.00 4.85
220 223 0.905337 CCAAGTTCCGAGTCCTCCCT 60.905 60.000 0.00 0.00 0.00 4.20
221 224 0.533032 CAAGTTCCGAGTCCTCCCTC 59.467 60.000 0.00 0.00 0.00 4.30
222 225 0.615261 AAGTTCCGAGTCCTCCCTCC 60.615 60.000 0.00 0.00 0.00 4.30
223 226 2.059190 GTTCCGAGTCCTCCCTCCC 61.059 68.421 0.00 0.00 0.00 4.30
226 229 2.695970 CCGAGTCCTCCCTCCCTCT 61.696 68.421 0.00 0.00 0.00 3.69
230 233 1.231928 GTCCTCCCTCCCTCTCTCC 59.768 68.421 0.00 0.00 0.00 3.71
260 267 1.682684 TCTTCCTCCTCCAGCGACC 60.683 63.158 0.00 0.00 0.00 4.79
375 386 4.436998 AGGTACGTGCTCAGCGGC 62.437 66.667 3.01 0.00 0.00 6.53
445 472 3.390521 TCGGCCTCGGTTGCATCT 61.391 61.111 0.00 0.00 36.95 2.90
447 474 3.512516 GGCCTCGGTTGCATCTGC 61.513 66.667 0.00 0.00 42.50 4.26
448 475 3.869272 GCCTCGGTTGCATCTGCG 61.869 66.667 0.00 0.00 45.83 5.18
568 606 2.355818 GGTAGTGGGGGATTTGTCAGAC 60.356 54.545 0.00 0.00 0.00 3.51
578 616 3.818773 GGATTTGTCAGACTTTTCGGGAA 59.181 43.478 1.31 0.00 0.00 3.97
583 621 6.945938 TTGTCAGACTTTTCGGGAATTTTA 57.054 33.333 1.31 0.00 0.00 1.52
585 623 6.908825 TGTCAGACTTTTCGGGAATTTTATG 58.091 36.000 1.31 0.00 0.00 1.90
586 624 6.072175 TGTCAGACTTTTCGGGAATTTTATGG 60.072 38.462 1.31 0.00 0.00 2.74
587 625 5.417580 TCAGACTTTTCGGGAATTTTATGGG 59.582 40.000 0.00 0.00 0.00 4.00
588 626 4.709886 AGACTTTTCGGGAATTTTATGGGG 59.290 41.667 0.00 0.00 0.00 4.96
589 627 3.772572 ACTTTTCGGGAATTTTATGGGGG 59.227 43.478 0.00 0.00 0.00 5.40
622 661 2.336945 TTACTCTAGATGCCGTCGGA 57.663 50.000 17.49 0.00 0.00 4.55
623 662 1.590932 TACTCTAGATGCCGTCGGAC 58.409 55.000 17.49 7.13 0.00 4.79
624 663 0.107116 ACTCTAGATGCCGTCGGACT 60.107 55.000 17.49 12.84 0.00 3.85
625 664 0.309302 CTCTAGATGCCGTCGGACTG 59.691 60.000 17.49 0.39 0.00 3.51
687 727 1.083401 GTAGATTGATTGCCGCGCG 60.083 57.895 25.67 25.67 0.00 6.86
743 783 3.252974 ACCGTGATCTGATGTTTCTCC 57.747 47.619 0.00 0.00 0.00 3.71
747 787 3.739519 CGTGATCTGATGTTTCTCCCCTC 60.740 52.174 0.00 0.00 0.00 4.30
755 795 5.012239 TGATGTTTCTCCCCTCTCAATTTG 58.988 41.667 0.00 0.00 0.00 2.32
756 796 3.157087 TGTTTCTCCCCTCTCAATTTGC 58.843 45.455 0.00 0.00 0.00 3.68
762 802 1.821136 CCCCTCTCAATTTGCTTGTCC 59.179 52.381 0.00 0.00 36.20 4.02
771 811 1.701031 TTTGCTTGTCCCAGGTCGGA 61.701 55.000 0.00 0.00 36.56 4.55
827 867 2.219325 CTGCTCTGGGTCTCGGTGAC 62.219 65.000 1.67 1.67 44.63 3.67
854 894 4.475444 CGGCTCCCCTCCCCTACA 62.475 72.222 0.00 0.00 0.00 2.74
855 895 2.768769 GGCTCCCCTCCCCTACAC 60.769 72.222 0.00 0.00 0.00 2.90
856 896 2.369001 GCTCCCCTCCCCTACACT 59.631 66.667 0.00 0.00 0.00 3.55
857 897 1.624753 GCTCCCCTCCCCTACACTA 59.375 63.158 0.00 0.00 0.00 2.74
858 898 0.759812 GCTCCCCTCCCCTACACTAC 60.760 65.000 0.00 0.00 0.00 2.73
954 994 0.460987 CAGGGGACGAGCAAGCTTAG 60.461 60.000 0.00 0.00 0.00 2.18
967 1007 0.317479 AGCTTAGTTCAGCGTCGGTT 59.683 50.000 0.00 0.00 45.24 4.44
968 1008 0.714439 GCTTAGTTCAGCGTCGGTTC 59.286 55.000 0.00 0.00 0.00 3.62
969 1009 0.982673 CTTAGTTCAGCGTCGGTTCG 59.017 55.000 0.00 0.00 0.00 3.95
999 1039 1.068250 GACTGATCTGGGCGGTAGC 59.932 63.158 4.49 0.00 44.18 3.58
1362 1402 5.495640 AGCATGAAGGAGAAGGAAGTAAAG 58.504 41.667 0.00 0.00 0.00 1.85
1395 1435 1.557099 TGGAGCTCGTGGACTATGTT 58.443 50.000 7.83 0.00 0.00 2.71
1407 1447 0.676782 ACTATGTTGCCTCGGCCAAC 60.677 55.000 2.24 10.17 41.09 3.77
1548 1588 1.890979 GCCTGTGATGGATCCTGCG 60.891 63.158 14.23 0.00 0.00 5.18
1638 1678 2.608090 GCTGGCTAAAAGGTACATCGAC 59.392 50.000 0.00 0.00 0.00 4.20
1659 1699 1.466167 CATTCGTTTGTCCTCAGGCTG 59.534 52.381 8.58 8.58 0.00 4.85
1936 1976 0.381801 ACTTCACAAGCCAAAGTGCG 59.618 50.000 0.00 0.00 35.76 5.34
1983 2023 5.001232 TCTTACTGCATTACCCAGTTTGTC 58.999 41.667 0.00 0.00 42.98 3.18
1995 2035 3.735746 CCCAGTTTGTCGAAAAAGATTGC 59.264 43.478 0.00 0.00 0.00 3.56
2001 2041 6.253512 AGTTTGTCGAAAAAGATTGCAAACTC 59.746 34.615 9.90 0.36 46.20 3.01
2058 2098 1.411977 CCCATCACAAACAGCACCAAA 59.588 47.619 0.00 0.00 0.00 3.28
2253 2294 3.151554 TCTGTGTTGCTTGATGCTTCAT 58.848 40.909 2.75 0.00 43.37 2.57
2257 2299 5.117584 TGTGTTGCTTGATGCTTCATTTTT 58.882 33.333 2.75 0.00 43.37 1.94
2264 2306 6.148150 TGCTTGATGCTTCATTTTTCATTTCC 59.852 34.615 2.75 0.00 43.37 3.13
2379 2422 2.291741 GGCATGGTAGTGCAGATTTAGC 59.708 50.000 0.00 0.00 46.81 3.09
2584 2628 5.106317 CCCTGTTATTTTGTGCTAACGACAT 60.106 40.000 0.00 0.00 31.83 3.06
2624 2668 4.454847 CACAATCTCTGACATCACAGCTTT 59.545 41.667 0.00 0.00 37.75 3.51
2803 2848 2.159787 GCACTGCGACTGACAACATTAG 60.160 50.000 0.00 0.00 0.00 1.73
2878 2927 3.839293 CAGTACTCTGGTTAGTGACTGC 58.161 50.000 0.00 0.00 37.97 4.40
2948 2997 4.518970 GGCACCTGACAAGATTCTGTTTAA 59.481 41.667 0.00 0.00 0.00 1.52
2950 2999 5.335191 GCACCTGACAAGATTCTGTTTAAGG 60.335 44.000 0.00 0.00 33.86 2.69
2974 3023 2.563620 TGTCTGTTTCGTGTGGGCTATA 59.436 45.455 0.00 0.00 0.00 1.31
3129 3178 9.846248 ATGTGAATAGAATCTTTACTTTGTTGC 57.154 29.630 0.00 0.00 0.00 4.17
3250 3301 0.820226 TCCAGGTTGCTGAGAGATCG 59.180 55.000 0.00 0.00 0.00 3.69
3388 3439 2.878406 TGTGCAAAGCCTCACTCTTAAC 59.122 45.455 0.00 0.00 34.49 2.01
3451 3502 2.186076 GAGTGTCTGCGGAAATACGAG 58.814 52.381 0.00 0.00 35.47 4.18
3481 3532 3.749226 AGCCAAAGAGAAGGAGAACAAG 58.251 45.455 0.00 0.00 0.00 3.16
3639 3695 7.055667 AGATGTTCCCCTTTTCTTTTCTTTC 57.944 36.000 0.00 0.00 0.00 2.62
3644 3700 5.766590 TCCCCTTTTCTTTTCTTTCTCTGT 58.233 37.500 0.00 0.00 0.00 3.41
3662 3718 3.007614 TCTGTTGGGTAGTTTGTAGCTCC 59.992 47.826 0.00 0.00 0.00 4.70
3705 3762 6.394345 AGAATTTCTTGAATCAGTAGGGGT 57.606 37.500 0.00 0.00 0.00 4.95
3910 3968 8.103305 TCATTGCTATATCCTTTATCCTTGTCC 58.897 37.037 0.00 0.00 0.00 4.02
3973 4031 1.212751 GTGGAAGCAAATGGTCGGC 59.787 57.895 0.00 0.00 0.00 5.54
3980 4038 1.081509 CAAATGGTCGGCCGTTGTG 60.082 57.895 27.15 11.06 42.86 3.33
3993 4051 1.004200 GTTGTGGTCGGTGGGTAGG 60.004 63.158 0.00 0.00 0.00 3.18
4192 4250 2.413837 CGTTCTGTTTCGTTGGAGGAT 58.586 47.619 0.00 0.00 0.00 3.24
4217 4278 4.222588 TCTGAATTGGCCATTTTAACCTGG 59.777 41.667 6.09 0.00 35.53 4.45
4259 4320 1.068474 AAATTCTCTGTTCGTCGCCG 58.932 50.000 0.00 0.00 0.00 6.46
4275 4336 1.820092 GCCGTAGCGTCAACTAGTAC 58.180 55.000 0.00 0.00 0.00 2.73
4276 4337 1.131126 GCCGTAGCGTCAACTAGTACA 59.869 52.381 0.00 0.00 0.00 2.90
4296 4357 6.992123 AGTACAATCTGTCTCACAAATCACAA 59.008 34.615 0.00 0.00 0.00 3.33
4319 4380 1.541588 GATTCAGAACAAGGTGGTGGC 59.458 52.381 0.00 0.00 0.00 5.01
4363 4430 0.035317 CCACCACAAGACTGCTGCTA 59.965 55.000 0.00 0.00 0.00 3.49
4366 4433 2.225019 CACCACAAGACTGCTGCTAAAG 59.775 50.000 0.00 0.00 0.00 1.85
4368 4435 1.808945 CACAAGACTGCTGCTAAAGGG 59.191 52.381 0.00 0.00 0.00 3.95
4379 4446 3.563390 GCTGCTAAAGGGTGAAGATGATC 59.437 47.826 0.00 0.00 0.00 2.92
4382 4449 4.141620 TGCTAAAGGGTGAAGATGATCCTC 60.142 45.833 0.00 0.00 0.00 3.71
4385 4452 2.837947 AGGGTGAAGATGATCCTCACA 58.162 47.619 21.77 1.37 33.41 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.364465 GGTCGCTTTTCTTTCTCTCTTGC 60.364 47.826 0.00 0.00 0.00 4.01
20 21 0.796927 CCGGGTCGCTTTTCTTTCTC 59.203 55.000 0.00 0.00 0.00 2.87
55 57 1.414378 GAAAAACAAATCCGTGGGCG 58.586 50.000 0.00 0.00 37.95 6.13
86 88 1.077644 CCCCTCTCTCTCCGACGAA 60.078 63.158 0.00 0.00 0.00 3.85
87 89 2.590645 CCCCTCTCTCTCCGACGA 59.409 66.667 0.00 0.00 0.00 4.20
88 90 2.517402 CCCCCTCTCTCTCCGACG 60.517 72.222 0.00 0.00 0.00 5.12
89 91 0.324460 TTTCCCCCTCTCTCTCCGAC 60.324 60.000 0.00 0.00 0.00 4.79
90 92 0.412244 TTTTCCCCCTCTCTCTCCGA 59.588 55.000 0.00 0.00 0.00 4.55
91 93 1.208293 CTTTTTCCCCCTCTCTCTCCG 59.792 57.143 0.00 0.00 0.00 4.63
164 167 4.682787 ACTTTTCTTTTCCTCCGCAAAAG 58.317 39.130 0.00 0.00 40.71 2.27
165 168 4.729227 ACTTTTCTTTTCCTCCGCAAAA 57.271 36.364 0.00 0.00 0.00 2.44
166 169 4.261447 GCTACTTTTCTTTTCCTCCGCAAA 60.261 41.667 0.00 0.00 0.00 3.68
167 170 3.252458 GCTACTTTTCTTTTCCTCCGCAA 59.748 43.478 0.00 0.00 0.00 4.85
168 171 2.812011 GCTACTTTTCTTTTCCTCCGCA 59.188 45.455 0.00 0.00 0.00 5.69
170 173 2.747989 GGGCTACTTTTCTTTTCCTCCG 59.252 50.000 0.00 0.00 0.00 4.63
171 174 3.759086 CTGGGCTACTTTTCTTTTCCTCC 59.241 47.826 0.00 0.00 0.00 4.30
172 175 3.191581 GCTGGGCTACTTTTCTTTTCCTC 59.808 47.826 0.00 0.00 0.00 3.71
173 176 3.157881 GCTGGGCTACTTTTCTTTTCCT 58.842 45.455 0.00 0.00 0.00 3.36
174 177 2.231478 GGCTGGGCTACTTTTCTTTTCC 59.769 50.000 0.00 0.00 0.00 3.13
175 178 2.890945 TGGCTGGGCTACTTTTCTTTTC 59.109 45.455 0.00 0.00 0.00 2.29
176 179 2.957474 TGGCTGGGCTACTTTTCTTTT 58.043 42.857 0.00 0.00 0.00 2.27
177 180 2.675658 TGGCTGGGCTACTTTTCTTT 57.324 45.000 0.00 0.00 0.00 2.52
178 181 2.519013 CTTGGCTGGGCTACTTTTCTT 58.481 47.619 0.00 0.00 0.00 2.52
179 182 1.272147 CCTTGGCTGGGCTACTTTTCT 60.272 52.381 0.00 0.00 0.00 2.52
195 198 1.608283 GGACTCGGAACTTGGACCTTG 60.608 57.143 0.00 0.00 0.00 3.61
220 223 2.691779 GGACGGAGGGAGAGAGGGA 61.692 68.421 0.00 0.00 0.00 4.20
221 224 2.123640 GGACGGAGGGAGAGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
222 225 2.123640 GGGACGGAGGGAGAGAGG 60.124 72.222 0.00 0.00 0.00 3.69
223 226 2.123640 GGGGACGGAGGGAGAGAG 60.124 72.222 0.00 0.00 0.00 3.20
524 558 1.081442 CCGAGAACAAAAAGGCGGC 60.081 57.895 0.00 0.00 31.80 6.53
536 574 2.693762 CCACTACCGCGACCGAGAA 61.694 63.158 8.23 0.00 36.29 2.87
568 606 4.400529 CCCCCATAAAATTCCCGAAAAG 57.599 45.455 0.00 0.00 0.00 2.27
586 624 1.146359 GTAAATCCCACCCATACCCCC 59.854 57.143 0.00 0.00 0.00 5.40
587 625 2.107726 GAGTAAATCCCACCCATACCCC 59.892 54.545 0.00 0.00 0.00 4.95
588 626 3.053826 AGAGTAAATCCCACCCATACCC 58.946 50.000 0.00 0.00 0.00 3.69
589 627 5.152934 TCTAGAGTAAATCCCACCCATACC 58.847 45.833 0.00 0.00 0.00 2.73
622 661 1.663702 CGCGAAACGGAGAACCAGT 60.664 57.895 0.00 0.00 38.44 4.00
623 662 0.736325 ATCGCGAAACGGAGAACCAG 60.736 55.000 15.24 0.00 43.89 4.00
624 663 1.011968 CATCGCGAAACGGAGAACCA 61.012 55.000 15.24 0.00 43.89 3.67
625 664 1.708027 CATCGCGAAACGGAGAACC 59.292 57.895 15.24 0.00 43.89 3.62
743 783 1.821136 GGGACAAGCAAATTGAGAGGG 59.179 52.381 0.00 0.00 41.83 4.30
747 787 2.229784 GACCTGGGACAAGCAAATTGAG 59.770 50.000 0.00 0.00 41.83 3.02
755 795 2.266055 CTCCGACCTGGGACAAGC 59.734 66.667 0.00 0.00 38.70 4.01
756 796 2.982130 CCTCCGACCTGGGACAAG 59.018 66.667 0.00 0.00 38.70 3.16
827 867 4.527583 GGGAGCCGAGCTGAGCTG 62.528 72.222 13.71 4.12 39.88 4.24
947 987 0.317479 ACCGACGCTGAACTAAGCTT 59.683 50.000 3.48 3.48 41.24 3.74
954 994 3.110178 CCCGAACCGACGCTGAAC 61.110 66.667 0.00 0.00 0.00 3.18
1234 1274 2.700773 CCTTAAAGCCCGGCAGCAC 61.701 63.158 13.15 0.00 34.23 4.40
1362 1402 0.235926 GCTCCAACAGAGTTTGTCGC 59.764 55.000 0.00 0.00 45.21 5.19
1395 1435 3.551496 CTTCTGGTTGGCCGAGGCA 62.551 63.158 16.65 0.00 44.11 4.75
1548 1588 0.110056 CAATCTGCAAGTGCGACCAC 60.110 55.000 0.00 0.00 45.83 4.16
1638 1678 0.804989 GCCTGAGGACAAACGAATGG 59.195 55.000 0.65 0.00 0.00 3.16
1659 1699 3.238108 TCGGAGTCAAAGAGATCAAGC 57.762 47.619 0.00 0.00 0.00 4.01
1830 1870 3.389329 TGATGCTCCCTAAGATCTCCAAC 59.611 47.826 0.00 0.00 0.00 3.77
1903 1943 0.322456 TGAAGTGGAATCAAGGCCCG 60.322 55.000 0.00 0.00 0.00 6.13
1936 1976 6.151691 ACAACTGTTGATGATACATTGCAAC 58.848 36.000 26.00 0.00 39.29 4.17
1983 2023 5.622856 GTCTGAGAGTTTGCAATCTTTTTCG 59.377 40.000 11.24 7.07 0.00 3.46
1995 2035 5.636965 CCTGATAACTGTGTCTGAGAGTTTG 59.363 44.000 0.00 0.00 38.97 2.93
2001 2041 2.419297 GCCCCTGATAACTGTGTCTGAG 60.419 54.545 3.12 0.00 0.00 3.35
2058 2098 3.395941 ACTCTCCCAAAAACATCACCTCT 59.604 43.478 0.00 0.00 0.00 3.69
2109 2149 2.975410 TGCATTTCTGAAACTCTGCG 57.025 45.000 17.46 1.75 32.42 5.18
2221 2262 6.643388 TCAAGCAACACAGATAGATGTATGT 58.357 36.000 0.00 0.00 0.00 2.29
2222 2263 7.573627 CATCAAGCAACACAGATAGATGTATG 58.426 38.462 0.00 0.00 0.00 2.39
2253 2294 9.883142 AAATTACACAACAGAGGAAATGAAAAA 57.117 25.926 0.00 0.00 0.00 1.94
2257 2299 8.231692 TGAAAATTACACAACAGAGGAAATGA 57.768 30.769 0.00 0.00 0.00 2.57
2264 2306 7.173907 AGGACAGATGAAAATTACACAACAGAG 59.826 37.037 0.00 0.00 0.00 3.35
2346 2389 5.300286 GCACTACCATGCCTTGAATAGAAAT 59.700 40.000 0.00 0.00 39.86 2.17
2379 2422 7.973388 ACCGGATAAATTGACACAATACAAATG 59.027 33.333 9.46 0.00 0.00 2.32
2600 2644 2.095532 GCTGTGATGTCAGAGATTGTGC 59.904 50.000 10.95 0.00 39.36 4.57
2602 2646 3.977134 AGCTGTGATGTCAGAGATTGT 57.023 42.857 10.95 0.00 39.36 2.71
2803 2848 4.552166 TGACTTTAGCACTTTGTTCTGC 57.448 40.909 0.00 0.00 0.00 4.26
2895 2944 6.013842 AGACAAAAGCCATAAACAGCTAAC 57.986 37.500 0.00 0.00 0.00 2.34
2948 2997 1.270839 CCACACGAAACAGACATCCCT 60.271 52.381 0.00 0.00 0.00 4.20
2950 2999 1.156736 CCCACACGAAACAGACATCC 58.843 55.000 0.00 0.00 0.00 3.51
2974 3023 4.103311 GTCCCTGAATTAGGTCATAGGCTT 59.897 45.833 0.00 0.00 45.80 4.35
3129 3178 2.775911 TTCATGAGTGCCTTCTCCAG 57.224 50.000 0.00 0.00 33.93 3.86
3250 3301 4.932200 TGGTCATTGTTCCACAAAAACAAC 59.068 37.500 3.76 0.00 46.19 3.32
3316 3367 3.072038 TCTCCAGTGCAGGGAATATGATG 59.928 47.826 8.31 0.00 33.11 3.07
3388 3439 1.069973 TCAGAGAACAATTTGCGCACG 60.070 47.619 11.12 0.86 0.00 5.34
3451 3502 1.620822 TCTCTTTGGCTTTGGCTTCC 58.379 50.000 0.00 0.00 38.73 3.46
3481 3532 0.886563 ATGTGGCTTCTTGCTTCAGC 59.113 50.000 0.00 0.00 42.39 4.26
3639 3695 4.246458 GAGCTACAAACTACCCAACAGAG 58.754 47.826 0.00 0.00 0.00 3.35
3644 3700 2.290071 GCAGGAGCTACAAACTACCCAA 60.290 50.000 0.00 0.00 37.91 4.12
3662 3718 9.630098 AAATTCTTACATTAGACACAATTGCAG 57.370 29.630 5.05 0.74 0.00 4.41
3705 3762 3.323691 TGTTTCACGAATCTCTGGAGGAA 59.676 43.478 0.00 0.00 0.00 3.36
3910 3968 3.367025 GGAACAGACTGTAACCGAATTCG 59.633 47.826 20.92 20.92 39.44 3.34
3980 4038 0.257039 TAGAGACCTACCCACCGACC 59.743 60.000 0.00 0.00 0.00 4.79
4131 4189 2.535012 TGAATGCACCTCACACGTTA 57.465 45.000 0.00 0.00 0.00 3.18
4166 4224 2.418628 CCAACGAAACAGAACGCCATAT 59.581 45.455 0.00 0.00 0.00 1.78
4180 4238 4.458989 CCAATTCAGAAATCCTCCAACGAA 59.541 41.667 0.00 0.00 0.00 3.85
4182 4240 3.428045 GCCAATTCAGAAATCCTCCAACG 60.428 47.826 0.00 0.00 0.00 4.10
4192 4250 6.229733 CAGGTTAAAATGGCCAATTCAGAAA 58.770 36.000 10.96 0.00 0.00 2.52
4259 4320 5.638783 ACAGATTGTACTAGTTGACGCTAC 58.361 41.667 0.00 0.00 0.00 3.58
4272 4333 6.785488 TGTGATTTGTGAGACAGATTGTAC 57.215 37.500 0.00 0.00 0.00 2.90
4273 4334 7.094677 CCATTGTGATTTGTGAGACAGATTGTA 60.095 37.037 0.00 0.00 0.00 2.41
4274 4335 6.294342 CCATTGTGATTTGTGAGACAGATTGT 60.294 38.462 0.00 0.00 0.00 2.71
4275 4336 6.072342 TCCATTGTGATTTGTGAGACAGATTG 60.072 38.462 0.00 0.00 0.00 2.67
4276 4337 6.005823 TCCATTGTGATTTGTGAGACAGATT 58.994 36.000 0.00 0.00 0.00 2.40
4296 4357 3.424703 CACCACCTTGTTCTGAATCCAT 58.575 45.455 0.00 0.00 0.00 3.41
4319 4380 6.130298 TGTTGTAATTCAGTTGAACTGTGG 57.870 37.500 23.17 0.00 46.03 4.17
4343 4404 1.227943 GCAGCAGTCTTGTGGTGGA 60.228 57.895 5.31 0.00 44.49 4.02
4385 4452 2.361610 CAGGAAAGGCCACGGCAT 60.362 61.111 10.83 0.00 44.11 4.40


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

AutoCloner maintained by Alex Coulton.