Multiple sequence alignment - TraesCS2A01G159400

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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 TraesCS2A01G159400 chr2A 100.000 3708 0 0 1 3708 107183915 107180208 0.000000e+00 6848.0
1 TraesCS2A01G159400 chr2A 81.250 112 16 3 791 897 773228761 773228872 6.600000e-13 86.1
2 TraesCS2A01G159400 chr2D 93.671 3097 109 35 1 3030 110844397 110841321 0.000000e+00 4553.0
3 TraesCS2A01G159400 chr2D 93.109 682 27 10 3029 3708 110841197 110840534 0.000000e+00 981.0
4 TraesCS2A01G159400 chr2D 92.157 51 1 3 3288 3335 115928262 115928312 6.640000e-08 69.4
5 TraesCS2A01G159400 chr2B 93.546 2789 146 19 398 3161 159971803 159969024 0.000000e+00 4122.0
6 TraesCS2A01G159400 chr2B 93.750 272 15 2 3369 3640 159969023 159968754 1.240000e-109 407.0
7 TraesCS2A01G159400 chr2B 91.979 187 9 3 209 394 159975388 159975207 1.320000e-64 257.0
8 TraesCS2A01G159400 chr2B 88.514 148 6 5 361 500 159971701 159971557 6.370000e-38 169.0
9 TraesCS2A01G159400 chr2B 81.250 112 17 4 791 900 496552672 496552563 1.830000e-13 87.9
10 TraesCS2A01G159400 chr2B 83.333 90 12 3 3302 3389 234630174 234630086 3.070000e-11 80.5
11 TraesCS2A01G159400 chr5D 85.128 1607 195 23 1140 2708 549548167 549546567 0.000000e+00 1604.0
12 TraesCS2A01G159400 chr5D 84.720 1610 205 23 1135 2709 549430087 549428484 0.000000e+00 1572.0
13 TraesCS2A01G159400 chr5D 84.606 864 107 13 1154 1994 549262020 549261160 0.000000e+00 835.0
14 TraesCS2A01G159400 chr5D 84.046 865 110 15 1154 1994 549229685 549228825 0.000000e+00 808.0
15 TraesCS2A01G159400 chr5D 89.809 157 14 2 53 208 539861024 539860869 2.260000e-47 200.0
16 TraesCS2A01G159400 chr5D 83.636 110 18 0 791 900 385720530 385720421 1.820000e-18 104.0
17 TraesCS2A01G159400 chr5B 89.112 845 86 1 1140 1978 701051716 701050872 0.000000e+00 1046.0
18 TraesCS2A01G159400 chr5B 84.393 865 107 17 1154 1994 700856493 700855633 0.000000e+00 824.0
19 TraesCS2A01G159400 chr5B 83.333 306 21 10 209 489 498071268 498071568 4.750000e-64 255.0
20 TraesCS2A01G159400 chr7D 83.800 858 103 21 1154 1977 162823648 162822793 0.000000e+00 782.0
21 TraesCS2A01G159400 chr7D 77.480 635 131 6 2062 2693 524251284 524251909 1.630000e-98 370.0
22 TraesCS2A01G159400 chr7D 79.739 306 35 9 209 488 460033680 460033376 2.920000e-46 196.0
23 TraesCS2A01G159400 chr7D 86.364 110 8 5 299 408 285420370 285420268 3.030000e-21 113.0
24 TraesCS2A01G159400 chrUn 82.032 807 133 9 1186 1983 75777180 75777983 0.000000e+00 676.0
25 TraesCS2A01G159400 chrUn 82.032 807 133 9 1186 1983 228925104 228924301 0.000000e+00 676.0
26 TraesCS2A01G159400 chrUn 77.532 632 130 9 2065 2693 76990009 76989387 1.630000e-98 370.0
27 TraesCS2A01G159400 chrUn 77.373 632 131 9 2065 2693 394209868 394209246 7.570000e-97 364.0
28 TraesCS2A01G159400 chrUn 77.373 632 131 9 2062 2690 401285993 401286615 7.570000e-97 364.0
29 TraesCS2A01G159400 chr7A 77.883 633 126 11 2062 2690 604252153 604252775 7.510000e-102 381.0
30 TraesCS2A01G159400 chr7A 77.251 633 130 11 2062 2690 604257554 604258176 3.520000e-95 359.0
31 TraesCS2A01G159400 chr7A 88.776 98 10 1 209 305 323484196 323484099 6.510000e-23 119.0
32 TraesCS2A01G159400 chr7A 85.455 110 10 4 299 408 323484059 323483956 3.920000e-20 110.0
33 TraesCS2A01G159400 chr6B 77.690 632 129 9 2065 2693 76420676 76420054 3.500000e-100 375.0
34 TraesCS2A01G159400 chr6B 78.330 563 108 8 2062 2620 95513644 95514196 5.890000e-93 351.0
35 TraesCS2A01G159400 chr6B 81.197 117 20 2 785 900 210961665 210961780 3.940000e-15 93.5
36 TraesCS2A01G159400 chr6B 80.342 117 21 2 785 900 210962057 210962172 1.830000e-13 87.9
37 TraesCS2A01G159400 chr6D 77.215 632 132 7 2065 2693 41622297 41621675 3.520000e-95 359.0
38 TraesCS2A01G159400 chr6A 76.025 634 135 11 2065 2693 52288025 52287404 2.780000e-81 313.0
39 TraesCS2A01G159400 chr1B 81.311 305 22 14 209 488 70239114 70238820 8.070000e-52 215.0
40 TraesCS2A01G159400 chr1B 84.211 114 13 5 791 901 466323723 466323612 5.060000e-19 106.0
41 TraesCS2A01G159400 chr4A 91.946 149 8 3 55 199 319821325 319821473 4.850000e-49 206.0
42 TraesCS2A01G159400 chr4A 80.909 110 17 4 793 900 743392994 743393101 2.370000e-12 84.2
43 TraesCS2A01G159400 chr5A 88.344 163 12 4 51 210 678207388 678207230 4.890000e-44 189.0
44 TraesCS2A01G159400 chr1D 88.514 148 14 2 54 199 381017612 381017466 3.810000e-40 176.0
45 TraesCS2A01G159400 chr4D 88.591 149 10 4 56 203 54056604 54056462 1.370000e-39 174.0
46 TraesCS2A01G159400 chr4D 77.500 120 19 6 3267 3382 509855000 509855115 8.600000e-07 65.8
47 TraesCS2A01G159400 chr7B 88.514 148 9 6 59 199 77429447 77429593 4.920000e-39 172.0
48 TraesCS2A01G159400 chr7B 87.075 147 16 1 56 199 680096237 680096091 2.960000e-36 163.0
49 TraesCS2A01G159400 chr1A 85.465 172 16 7 47 213 516784113 516783946 1.770000e-38 171.0
50 TraesCS2A01G159400 chr4B 84.516 155 21 2 49 203 474333628 474333779 2.310000e-32 150.0
51 TraesCS2A01G159400 chr3A 85.542 83 12 0 3300 3382 180033277 180033359 1.830000e-13 87.9


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 TraesCS2A01G159400 chr2A 107180208 107183915 3707 True 6848.00 6848 100.00000 1 3708 1 chr2A.!!$R1 3707
1 TraesCS2A01G159400 chr2D 110840534 110844397 3863 True 2767.00 4553 93.39000 1 3708 2 chr2D.!!$R1 3707
2 TraesCS2A01G159400 chr2B 159968754 159975388 6634 True 1238.75 4122 91.94725 209 3640 4 chr2B.!!$R3 3431
3 TraesCS2A01G159400 chr5D 549546567 549548167 1600 True 1604.00 1604 85.12800 1140 2708 1 chr5D.!!$R6 1568
4 TraesCS2A01G159400 chr5D 549428484 549430087 1603 True 1572.00 1572 84.72000 1135 2709 1 chr5D.!!$R5 1574
5 TraesCS2A01G159400 chr5D 549261160 549262020 860 True 835.00 835 84.60600 1154 1994 1 chr5D.!!$R4 840
6 TraesCS2A01G159400 chr5D 549228825 549229685 860 True 808.00 808 84.04600 1154 1994 1 chr5D.!!$R3 840
7 TraesCS2A01G159400 chr5B 701050872 701051716 844 True 1046.00 1046 89.11200 1140 1978 1 chr5B.!!$R2 838
8 TraesCS2A01G159400 chr5B 700855633 700856493 860 True 824.00 824 84.39300 1154 1994 1 chr5B.!!$R1 840
9 TraesCS2A01G159400 chr7D 162822793 162823648 855 True 782.00 782 83.80000 1154 1977 1 chr7D.!!$R1 823
10 TraesCS2A01G159400 chr7D 524251284 524251909 625 False 370.00 370 77.48000 2062 2693 1 chr7D.!!$F1 631
11 TraesCS2A01G159400 chrUn 75777180 75777983 803 False 676.00 676 82.03200 1186 1983 1 chrUn.!!$F1 797
12 TraesCS2A01G159400 chrUn 228924301 228925104 803 True 676.00 676 82.03200 1186 1983 1 chrUn.!!$R2 797
13 TraesCS2A01G159400 chrUn 76989387 76990009 622 True 370.00 370 77.53200 2065 2693 1 chrUn.!!$R1 628
14 TraesCS2A01G159400 chrUn 394209246 394209868 622 True 364.00 364 77.37300 2065 2693 1 chrUn.!!$R3 628
15 TraesCS2A01G159400 chrUn 401285993 401286615 622 False 364.00 364 77.37300 2062 2690 1 chrUn.!!$F2 628
16 TraesCS2A01G159400 chr7A 604252153 604252775 622 False 381.00 381 77.88300 2062 2690 1 chr7A.!!$F1 628
17 TraesCS2A01G159400 chr7A 604257554 604258176 622 False 359.00 359 77.25100 2062 2690 1 chr7A.!!$F2 628
18 TraesCS2A01G159400 chr6B 76420054 76420676 622 True 375.00 375 77.69000 2065 2693 1 chr6B.!!$R1 628
19 TraesCS2A01G159400 chr6B 95513644 95514196 552 False 351.00 351 78.33000 2062 2620 1 chr6B.!!$F1 558
20 TraesCS2A01G159400 chr6D 41621675 41622297 622 True 359.00 359 77.21500 2065 2693 1 chr6D.!!$R1 628
21 TraesCS2A01G159400 chr6A 52287404 52288025 621 True 313.00 313 76.02500 2065 2693 1 chr6A.!!$R1 628

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
937 4390 0.325933 ATAGCAGCACACCAAGCTCA 59.674 50.0 0.0 0.0 41.14 4.26 F
951 4404 0.663153 AGCTCAACTCGTTTGGCAAC 59.337 50.0 0.0 0.0 35.16 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 5365 0.109735 GCTCGTCGATGACTGTGTCA 60.110 55.0 2.39 2.77 46.90 3.58 R
2857 6431 0.754957 CAAACAACTCTGGCCCACCA 60.755 55.0 0.00 0.00 46.51 4.17 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
61 62 6.834168 TCCATCAATAAAAGAAAGGGTGTC 57.166 37.500 0.00 0.00 0.00 3.67
78 79 1.301423 GTCGCTAGGTCTCAGTCGAT 58.699 55.000 0.00 0.00 0.00 3.59
107 113 7.939039 AGATTTAACCAAGTCTCAATCAAGTGA 59.061 33.333 0.00 0.00 0.00 3.41
117 123 6.093219 AGTCTCAATCAAGTGACATAACATGC 59.907 38.462 0.00 0.00 35.17 4.06
127 133 6.233434 AGTGACATAACATGCAAGAGAGAAA 58.767 36.000 0.00 0.00 0.00 2.52
167 175 4.944962 TTTGCACGGATCTCAATGTAAG 57.055 40.909 0.00 0.00 0.00 2.34
194 228 7.112779 TCTTATGGATATAGCATCGACTGAGA 58.887 38.462 0.00 0.00 0.00 3.27
287 322 9.294030 CCATTGACAAAAAGTAATGCTTCTATC 57.706 33.333 0.00 0.00 36.17 2.08
315 350 8.466798 AGACTTCCCACGGAAATAATTATTTTG 58.533 33.333 21.39 18.60 41.54 2.44
355 390 8.509690 TGAAAGCACATCTCAATCTAAAAAGAG 58.490 33.333 0.00 0.00 0.00 2.85
665 4103 1.815421 CGGGAAGCGAACCATCCAG 60.815 63.158 0.00 0.00 34.82 3.86
681 4119 3.728076 TCCAGAATTAGCGCTCGTTAT 57.272 42.857 16.34 4.32 0.00 1.89
682 4120 3.381045 TCCAGAATTAGCGCTCGTTATG 58.619 45.455 16.34 17.12 0.00 1.90
712 4150 1.064389 GCAGGTCCTAGGAGGCAAATT 60.064 52.381 13.15 0.00 34.61 1.82
731 4170 1.174783 TGTACGTCCTGCTTCCTCTC 58.825 55.000 0.00 0.00 0.00 3.20
734 4173 0.534412 ACGTCCTGCTTCCTCTCATG 59.466 55.000 0.00 0.00 0.00 3.07
764 4203 2.005266 AGGTGGGCTGATGGATGCT 61.005 57.895 0.00 0.00 0.00 3.79
806 4245 6.626302 TGACTTCATCCGAAAAAGTTTGTTT 58.374 32.000 0.00 0.00 33.54 2.83
809 4248 7.320399 ACTTCATCCGAAAAAGTTTGTTTCTT 58.680 30.769 0.00 0.00 33.63 2.52
852 4291 6.992715 ACTAATTTGGTGCTAGATACATCCAC 59.007 38.462 0.00 0.00 0.00 4.02
855 4294 4.406648 TGGTGCTAGATACATCCACTTG 57.593 45.455 0.00 0.00 0.00 3.16
861 4307 5.300539 TGCTAGATACATCCACTTGAGAGAC 59.699 44.000 0.00 0.00 0.00 3.36
887 4336 3.254470 TGAGACAAACTTGTTCGGACA 57.746 42.857 0.00 0.00 42.43 4.02
936 4389 2.208431 CTATAGCAGCACACCAAGCTC 58.792 52.381 0.00 0.00 41.14 4.09
937 4390 0.325933 ATAGCAGCACACCAAGCTCA 59.674 50.000 0.00 0.00 41.14 4.26
951 4404 0.663153 AGCTCAACTCGTTTGGCAAC 59.337 50.000 0.00 0.00 35.16 4.17
1902 5431 0.244178 GAAGGGAGCTCGACGACTTT 59.756 55.000 7.83 0.00 0.00 2.66
1978 5507 1.372997 GAGGTCAAAGCGCACTCGA 60.373 57.895 11.47 0.00 38.10 4.04
2015 5544 9.106977 TCCACACTTTATATATACAAGGGCATA 57.893 33.333 12.84 2.15 0.00 3.14
2191 5764 3.307906 CGGGTGGTGGGTCGAGAA 61.308 66.667 0.00 0.00 0.00 2.87
2236 5809 1.539388 CCGCAACTCAACTATGCCAAA 59.461 47.619 0.00 0.00 36.75 3.28
2294 5867 1.675310 CCCTTCAATCTGCCGCACA 60.675 57.895 0.00 0.00 0.00 4.57
2857 6431 7.341256 ACTGCCATCAACATCTAATTGATCTTT 59.659 33.333 0.00 0.00 43.39 2.52
2882 6456 2.293399 GGGCCAGAGTTGTTTGTAACAG 59.707 50.000 4.39 0.00 43.27 3.16
2929 6503 9.255304 TCCTACAAAAACAAAATTGCATTACTC 57.745 29.630 0.00 0.00 0.00 2.59
3091 6790 9.908152 CTACCTCCTTTGTTTTAAAATGTAAGG 57.092 33.333 21.12 21.12 33.61 2.69
3151 6850 5.954296 AACATCAGACATTTTGAGACAGG 57.046 39.130 0.00 0.00 0.00 4.00
3163 6862 9.220906 ACATTTTGAGACAGGGGTAGTATATAA 57.779 33.333 0.00 0.00 0.00 0.98
3304 7007 9.650539 GATGCTTATATACACTCACTCATGAAT 57.349 33.333 0.00 0.00 33.30 2.57
3309 7012 2.071540 ACACTCACTCATGAATGCACG 58.928 47.619 0.00 0.00 35.41 5.34
3316 7019 2.147749 CATGAATGCACGCACGCAC 61.148 57.895 0.00 0.00 46.56 5.34
3317 7020 2.615387 ATGAATGCACGCACGCACA 61.615 52.632 0.00 0.00 46.56 4.57
3318 7021 2.784957 ATGAATGCACGCACGCACAC 62.785 55.000 0.00 0.00 46.56 3.82
3319 7022 4.326766 AATGCACGCACGCACACC 62.327 61.111 0.00 0.00 46.56 4.16
3323 7026 2.434185 CACGCACGCACACCCTAT 60.434 61.111 0.00 0.00 0.00 2.57
3324 7027 2.125673 ACGCACGCACACCCTATC 60.126 61.111 0.00 0.00 0.00 2.08
3325 7028 2.890474 CGCACGCACACCCTATCC 60.890 66.667 0.00 0.00 0.00 2.59
3326 7029 2.584608 GCACGCACACCCTATCCT 59.415 61.111 0.00 0.00 0.00 3.24
3327 7030 1.820581 GCACGCACACCCTATCCTA 59.179 57.895 0.00 0.00 0.00 2.94
3328 7031 0.393077 GCACGCACACCCTATCCTAT 59.607 55.000 0.00 0.00 0.00 2.57
3329 7032 1.873903 GCACGCACACCCTATCCTATG 60.874 57.143 0.00 0.00 0.00 2.23
3330 7033 1.686587 CACGCACACCCTATCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
3331 7034 1.964223 ACGCACACCCTATCCTATGAG 59.036 52.381 0.00 0.00 0.00 2.90
3332 7035 1.337260 CGCACACCCTATCCTATGAGC 60.337 57.143 0.00 0.00 0.00 4.26
3333 7036 1.694150 GCACACCCTATCCTATGAGCA 59.306 52.381 0.00 0.00 0.00 4.26
3334 7037 2.548920 GCACACCCTATCCTATGAGCAC 60.549 54.545 0.00 0.00 0.00 4.40
3335 7038 2.037772 CACACCCTATCCTATGAGCACC 59.962 54.545 0.00 0.00 0.00 5.01
3336 7039 1.625818 CACCCTATCCTATGAGCACCC 59.374 57.143 0.00 0.00 0.00 4.61
3353 7056 2.279069 CCCGAGGACACTGAGCTGT 61.279 63.158 0.00 0.00 0.00 4.40
3359 7062 1.202580 AGGACACTGAGCTGTCACAAC 60.203 52.381 14.09 1.48 42.17 3.32
3407 7110 1.400242 GCATCTTGCGGTCAACAGAAC 60.400 52.381 0.00 0.00 31.71 3.01
3434 7137 9.753674 TCTTACTGAAGGAACCATTTGAATTAT 57.246 29.630 0.00 0.00 33.09 1.28
3494 7197 7.251321 ACTGGTTCTCTCACAAGAAATCTAT 57.749 36.000 0.00 0.00 37.04 1.98
3496 7199 7.180051 ACTGGTTCTCTCACAAGAAATCTATCT 59.820 37.037 0.00 0.00 37.04 1.98
3587 7290 9.845740 ATCTACCAATTATGCAATGTGTAGTAA 57.154 29.630 0.00 0.00 34.15 2.24
3656 7359 0.107848 TAGCTAACCGGCTCCTTTGC 60.108 55.000 0.00 0.37 42.97 3.68
3664 7367 2.980233 GCTCCTTTGCCGTGCAGT 60.980 61.111 0.00 0.00 40.61 4.40
3690 7393 1.749063 CGTCAGGGATGCTACAGTACA 59.251 52.381 0.00 0.00 0.00 2.90
3696 7399 0.104304 GATGCTACAGTACACCGGGG 59.896 60.000 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.941873 CCTAGCGACACCCTTTCTTTTATT 59.058 41.667 0.00 0.00 0.00 1.40
52 53 0.896226 GAGACCTAGCGACACCCTTT 59.104 55.000 0.00 0.00 0.00 3.11
61 62 1.671328 TCAATCGACTGAGACCTAGCG 59.329 52.381 0.00 0.00 0.00 4.26
99 105 6.175471 TCTCTTGCATGTTATGTCACTTGAT 58.825 36.000 0.00 0.00 0.00 2.57
107 113 7.750229 TCTTTTTCTCTCTTGCATGTTATGT 57.250 32.000 0.00 0.00 0.00 2.29
152 160 7.606349 TCCATAAGATCTTACATTGAGATCCG 58.394 38.462 17.35 0.00 46.88 4.18
167 175 7.935520 TCAGTCGATGCTATATCCATAAGATC 58.064 38.462 0.00 0.00 36.33 2.75
194 228 7.162082 AGCATACTTTTACAGTCTTGCTAAGT 58.838 34.615 6.98 0.00 46.16 2.24
287 322 3.343941 TTATTTCCGTGGGAAGTCTGG 57.656 47.619 0.00 0.00 43.06 3.86
315 350 9.410556 AGATGTGCTTTCAATAAACAAATACAC 57.589 29.630 0.00 0.00 0.00 2.90
355 390 6.652245 CATTTTTGTGCAAGGAAACATCTTC 58.348 36.000 0.00 0.00 0.00 2.87
549 3987 1.547372 CAACTTCTGATTTGCCCCCAG 59.453 52.381 0.00 0.00 0.00 4.45
554 3992 5.705609 TTCCTAACAACTTCTGATTTGCC 57.294 39.130 0.71 0.00 0.00 4.52
563 4001 9.201127 ACGTCTAATTAGTTTCCTAACAACTTC 57.799 33.333 12.19 0.00 36.03 3.01
638 4076 3.002102 GGTTCGCTTCCCGTTAATTACA 58.998 45.455 0.00 0.00 38.35 2.41
654 4092 1.261619 GCGCTAATTCTGGATGGTTCG 59.738 52.381 0.00 0.00 0.00 3.95
665 4103 3.381949 AGGACATAACGAGCGCTAATTC 58.618 45.455 11.50 0.00 0.00 2.17
681 4119 2.276116 GGACCTGCGTGAGAGGACA 61.276 63.158 0.00 0.00 34.08 4.02
682 4120 0.680280 TAGGACCTGCGTGAGAGGAC 60.680 60.000 3.53 0.00 34.08 3.85
712 4150 1.174783 GAGAGGAAGCAGGACGTACA 58.825 55.000 0.00 0.00 0.00 2.90
734 4173 2.742372 CCACCTGTGCACCGTAGC 60.742 66.667 15.69 0.00 0.00 3.58
787 4226 9.810545 ATTTAAGAAACAAACTTTTTCGGATGA 57.189 25.926 0.00 0.00 37.91 2.92
836 4275 5.300539 TCTCTCAAGTGGATGTATCTAGCAC 59.699 44.000 0.00 0.00 0.00 4.40
855 4294 6.670077 AAGTTTGTCTCAAACTTGTCTCTC 57.330 37.500 28.03 3.71 45.58 3.20
887 4336 5.576822 GCATGAGTCCCTATATACTCCCTCT 60.577 48.000 0.00 0.00 41.19 3.69
936 4389 2.541588 CCTCTTGTTGCCAAACGAGTTG 60.542 50.000 5.90 0.00 44.96 3.16
937 4390 1.676006 CCTCTTGTTGCCAAACGAGTT 59.324 47.619 5.90 0.00 44.96 3.01
951 4404 3.873952 GCTTCCTAATGTAGCACCTCTTG 59.126 47.826 0.00 0.00 35.05 3.02
954 4407 3.462021 CTGCTTCCTAATGTAGCACCTC 58.538 50.000 0.00 0.00 39.79 3.85
1126 4610 1.209127 CCGACGCACCAACAATTCC 59.791 57.895 0.00 0.00 0.00 3.01
1647 5164 4.388499 GGCCGAGGCTCACCGAAA 62.388 66.667 15.95 0.00 42.76 3.46
1836 5365 0.109735 GCTCGTCGATGACTGTGTCA 60.110 55.000 2.39 2.77 46.90 3.58
2015 5544 3.627123 GGAAGCCTTTTTGTTTTGCATGT 59.373 39.130 0.00 0.00 0.00 3.21
2191 5764 2.045926 GATTCCTGCACCAGCCGT 60.046 61.111 0.00 0.00 41.13 5.68
2269 5842 1.299648 CAGATTGAAGGGGGCGACA 59.700 57.895 0.00 0.00 0.00 4.35
2294 5867 1.079197 TGGTGTCATCGAGCGCAAT 60.079 52.632 11.47 0.00 0.00 3.56
2788 6361 8.357402 ACCTCTTGTTTAATAACATTGTGAACC 58.643 33.333 0.00 0.00 43.43 3.62
2857 6431 0.754957 CAAACAACTCTGGCCCACCA 60.755 55.000 0.00 0.00 46.51 4.17
2938 6512 9.701098 ATCGTGACTTGATTACTTGTAGTTTTA 57.299 29.630 0.00 0.00 0.00 1.52
2939 6513 8.495949 CATCGTGACTTGATTACTTGTAGTTTT 58.504 33.333 0.00 0.00 0.00 2.43
3260 6961 9.712305 ATAAGCATCTGTAATTGTACTATGTCC 57.288 33.333 0.00 0.00 31.87 4.02
3287 6988 3.867493 CGTGCATTCATGAGTGAGTGTAT 59.133 43.478 21.28 0.00 42.29 2.29
3309 7012 0.393077 ATAGGATAGGGTGTGCGTGC 59.607 55.000 0.00 0.00 0.00 5.34
3316 7019 1.625818 GGGTGCTCATAGGATAGGGTG 59.374 57.143 0.00 0.00 0.00 4.61
3317 7020 1.485210 GGGGTGCTCATAGGATAGGGT 60.485 57.143 0.00 0.00 0.00 4.34
3318 7021 1.280457 GGGGTGCTCATAGGATAGGG 58.720 60.000 0.00 0.00 0.00 3.53
3319 7022 0.898320 CGGGGTGCTCATAGGATAGG 59.102 60.000 0.00 0.00 0.00 2.57
3320 7023 1.821753 CTCGGGGTGCTCATAGGATAG 59.178 57.143 0.00 0.00 0.00 2.08
3321 7024 1.550179 CCTCGGGGTGCTCATAGGATA 60.550 57.143 0.00 0.00 0.00 2.59
3322 7025 0.833834 CCTCGGGGTGCTCATAGGAT 60.834 60.000 0.00 0.00 0.00 3.24
3323 7026 1.457643 CCTCGGGGTGCTCATAGGA 60.458 63.158 0.00 0.00 0.00 2.94
3324 7027 1.457643 TCCTCGGGGTGCTCATAGG 60.458 63.158 0.00 0.00 0.00 2.57
3325 7028 1.043116 TGTCCTCGGGGTGCTCATAG 61.043 60.000 0.00 0.00 0.00 2.23
3326 7029 1.001120 TGTCCTCGGGGTGCTCATA 59.999 57.895 0.00 0.00 0.00 2.15
3327 7030 2.284625 TGTCCTCGGGGTGCTCAT 60.285 61.111 0.00 0.00 0.00 2.90
3328 7031 3.311110 GTGTCCTCGGGGTGCTCA 61.311 66.667 0.00 0.00 0.00 4.26
3329 7032 2.997897 AGTGTCCTCGGGGTGCTC 60.998 66.667 0.00 0.00 0.00 4.26
3330 7033 3.314331 CAGTGTCCTCGGGGTGCT 61.314 66.667 0.00 0.00 0.00 4.40
3331 7034 3.302347 CTCAGTGTCCTCGGGGTGC 62.302 68.421 0.00 0.00 0.00 5.01
3332 7035 2.973899 CTCAGTGTCCTCGGGGTG 59.026 66.667 0.00 0.00 0.00 4.61
3333 7036 2.997897 GCTCAGTGTCCTCGGGGT 60.998 66.667 0.00 0.00 0.00 4.95
3334 7037 2.681778 AGCTCAGTGTCCTCGGGG 60.682 66.667 0.00 0.00 0.00 5.73
3335 7038 2.219325 GACAGCTCAGTGTCCTCGGG 62.219 65.000 0.00 0.00 40.96 5.14
3336 7039 1.214062 GACAGCTCAGTGTCCTCGG 59.786 63.158 0.00 0.00 40.96 4.63
3353 7056 7.944061 ACTTCATCAATCTCAAAATGTTGTGA 58.056 30.769 2.96 2.96 40.50 3.58
3359 7062 6.025896 CGGTGACTTCATCAATCTCAAAATG 58.974 40.000 0.00 0.00 39.72 2.32
3400 7103 5.130477 TGGTTCCTTCAGTAAGAGTTCTGTT 59.870 40.000 0.00 0.00 34.37 3.16
3407 7110 7.693969 ATTCAAATGGTTCCTTCAGTAAGAG 57.306 36.000 0.00 0.00 34.37 2.85
3586 7289 7.170998 GTGCTGCCGTATATTTTACAGACTATT 59.829 37.037 0.00 0.00 0.00 1.73
3587 7290 6.645415 GTGCTGCCGTATATTTTACAGACTAT 59.355 38.462 0.00 0.00 0.00 2.12
3600 7303 2.073056 CACAACTTGTGCTGCCGTATA 58.927 47.619 8.97 0.00 41.89 1.47
3664 7367 0.613572 TAGCATCCCTGACGTGTCCA 60.614 55.000 0.00 0.00 0.00 4.02
3690 7393 2.031465 CGTTTACACTGCCCCGGT 59.969 61.111 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.