Multiple sequence alignment - TraesCS5B01G073200

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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 TraesCS5B01G073200 chr5B 100.000 4745 0 0 1 4745 87227739 87232483 0.000000e+00 8763
1 TraesCS5B01G073200 chr5B 92.029 138 6 3 4612 4745 672545669 672545533 6.270000e-44 189
2 TraesCS5B01G073200 chr5D 96.139 4377 122 16 385 4745 77576942 77581287 0.000000e+00 7103
3 TraesCS5B01G073200 chr5D 90.296 371 14 15 19 384 77576538 77576891 2.590000e-127 466
4 TraesCS5B01G073200 chr5A 94.288 4412 139 40 385 4745 74477277 74481626 0.000000e+00 6647
5 TraesCS5B01G073200 chr5A 90.339 383 10 15 19 381 74476861 74477236 1.190000e-130 477
6 TraesCS5B01G073200 chr6B 92.754 138 5 3 4612 4745 599816942 599817078 1.350000e-45 195
7 TraesCS5B01G073200 chr2B 92.754 138 5 3 4612 4745 183539326 183539190 1.350000e-45 195


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 TraesCS5B01G073200 chr5B 87227739 87232483 4744 False 8763.0 8763 100.0000 1 4745 1 chr5B.!!$F1 4744
1 TraesCS5B01G073200 chr5D 77576538 77581287 4749 False 3784.5 7103 93.2175 19 4745 2 chr5D.!!$F1 4726
2 TraesCS5B01G073200 chr5A 74476861 74481626 4765 False 3562.0 6647 92.3135 19 4745 2 chr5A.!!$F1 4726

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
695 801 0.03601 ACCTGAGATTTCTGCACCCG 60.036 55.0 0.0 0.0 0.0 5.28 F
2283 2405 0.25077 AAACGGAGGGGCTTGAAGAC 60.251 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2477 0.314302 GAGCAGACGTGTACACACCT 59.686 55.000 24.98 17.19 43.66 4.00 R
4131 4261 1.741706 GGACAGTCATCCAGCAACATG 59.258 52.381 2.17 0.00 38.77 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
17 18 3.249189 GTGTGTGAGCCCCAGGGA 61.249 66.667 7.25 0.00 37.50 4.20
107 109 1.120530 ACCCGGTGGATGCTACTAAG 58.879 55.000 0.00 0.00 34.81 2.18
108 110 1.342674 ACCCGGTGGATGCTACTAAGA 60.343 52.381 0.00 0.00 34.81 2.10
109 111 1.341531 CCCGGTGGATGCTACTAAGAG 59.658 57.143 0.00 0.00 0.00 2.85
110 112 1.269831 CCGGTGGATGCTACTAAGAGC 60.270 57.143 0.00 0.00 43.16 4.09
117 119 3.762674 GCTACTAAGAGCACCCCAC 57.237 57.895 0.00 0.00 42.36 4.61
198 209 3.198489 GCGAGGCAAGGCAGTAGC 61.198 66.667 0.00 0.00 41.10 3.58
201 212 2.045536 AGGCAAGGCAGTAGCAGC 60.046 61.111 0.00 0.00 44.61 5.25
204 215 3.048941 GCAAGGCAGTAGCAGCAGC 62.049 63.158 0.00 0.00 44.61 5.25
205 216 1.673337 CAAGGCAGTAGCAGCAGCA 60.673 57.895 3.17 0.00 45.49 4.41
206 217 1.376942 AAGGCAGTAGCAGCAGCAG 60.377 57.895 3.17 0.00 45.49 4.24
207 218 2.046507 GGCAGTAGCAGCAGCAGT 60.047 61.111 3.17 0.00 45.49 4.40
208 219 1.219124 GGCAGTAGCAGCAGCAGTA 59.781 57.895 3.17 0.00 45.49 2.74
209 220 0.809241 GGCAGTAGCAGCAGCAGTAG 60.809 60.000 3.17 0.00 45.49 2.57
210 221 0.108424 GCAGTAGCAGCAGCAGTAGT 60.108 55.000 3.17 0.00 45.49 2.73
212 223 0.534412 AGTAGCAGCAGCAGTAGTGG 59.466 55.000 3.17 0.00 45.49 4.00
214 225 1.476891 GTAGCAGCAGCAGTAGTGGTA 59.523 52.381 3.17 0.00 45.49 3.25
239 258 2.904434 AGTGTAGTACAAACAGGGGGAG 59.096 50.000 4.11 0.00 0.00 4.30
250 269 2.428901 ACAGGGGGAGAAAAGGAAAGA 58.571 47.619 0.00 0.00 0.00 2.52
381 406 1.456705 GAGCGGGGAGGATCTGAGT 60.457 63.158 0.00 0.00 33.73 3.41
382 407 1.743321 GAGCGGGGAGGATCTGAGTG 61.743 65.000 0.00 0.00 33.73 3.51
383 408 1.758514 GCGGGGAGGATCTGAGTGA 60.759 63.158 0.00 0.00 33.73 3.41
395 479 2.319844 TCTGAGTGACCTTGCTCTTGA 58.680 47.619 0.00 0.00 33.22 3.02
420 506 1.345741 TCCACTGGTTTGAGAGAGCAG 59.654 52.381 0.00 2.14 45.52 4.24
495 581 6.199719 GTCAAATCTTTGCTGAGGTTTCTTTG 59.800 38.462 0.00 0.00 38.05 2.77
560 650 1.673477 CCAAAAGCCAAAGCCCTCC 59.327 57.895 0.00 0.00 41.25 4.30
610 709 0.178938 TTGCATTTCAAGCCCTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
621 720 3.083997 CCTCCCAACCCTCCTCCG 61.084 72.222 0.00 0.00 0.00 4.63
631 730 1.203199 ACCCTCCTCCGTTTCTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
694 800 2.087646 GAACCTGAGATTTCTGCACCC 58.912 52.381 0.00 0.00 0.00 4.61
695 801 0.036010 ACCTGAGATTTCTGCACCCG 60.036 55.000 0.00 0.00 0.00 5.28
696 802 1.372087 CCTGAGATTTCTGCACCCGC 61.372 60.000 0.00 0.00 39.24 6.13
735 852 1.072331 TGTTCTTGGTTGAGGGCTCTC 59.928 52.381 6.66 6.66 40.36 3.20
755 872 3.887716 CTCACATTTCTGATCCCCCATTC 59.112 47.826 0.00 0.00 0.00 2.67
959 1077 4.700365 GGCGCTGCGGTTGGTTTC 62.700 66.667 24.61 3.75 0.00 2.78
960 1078 4.700365 GCGCTGCGGTTGGTTTCC 62.700 66.667 24.61 0.00 0.00 3.13
961 1079 4.038080 CGCTGCGGTTGGTTTCCC 62.038 66.667 15.40 0.00 0.00 3.97
962 1080 3.680786 GCTGCGGTTGGTTTCCCC 61.681 66.667 0.00 0.00 0.00 4.81
1383 1502 1.771255 GCCACCTTCCTCTCCATGTAT 59.229 52.381 0.00 0.00 0.00 2.29
1523 1645 1.760480 GCTGGGACTCCTCCTCCTC 60.760 68.421 0.00 0.00 36.68 3.71
1524 1646 1.454847 CTGGGACTCCTCCTCCTCG 60.455 68.421 0.00 0.00 36.68 4.63
1525 1647 2.218115 CTGGGACTCCTCCTCCTCGT 62.218 65.000 0.00 0.00 36.68 4.18
1716 1838 3.006756 GCTCGCTGAGTGCTACCCA 62.007 63.158 7.27 0.00 40.11 4.51
1886 2008 0.984230 AAGGAGATCGTGGGCAAGAA 59.016 50.000 0.00 0.00 0.00 2.52
2007 2129 0.613853 AGCAGAATGGCTGGCATGTT 60.614 50.000 17.99 3.39 43.89 2.71
2073 2195 4.069232 CTCTCGCTGTTCCGGCCA 62.069 66.667 2.24 0.00 31.00 5.36
2098 2220 9.482627 CAGACTTCATTATAACCTCATTCTACC 57.517 37.037 0.00 0.00 0.00 3.18
2160 2282 6.409704 TCTGATCAAGAAGTCAGTTATTGGG 58.590 40.000 0.00 0.00 41.92 4.12
2202 2324 0.685458 GCAATGCCTCTGGGATGGTT 60.685 55.000 0.00 0.00 32.99 3.67
2214 2336 2.922955 TGGGATGGTTAGGATTGTTCCA 59.077 45.455 0.00 0.00 45.30 3.53
2268 2390 3.899734 TGAATTTGATGCAGTGGAAACG 58.100 40.909 0.00 0.00 0.00 3.60
2274 2396 2.359975 GCAGTGGAAACGGAGGGG 60.360 66.667 0.00 0.00 0.00 4.79
2283 2405 0.250770 AAACGGAGGGGCTTGAAGAC 60.251 55.000 0.00 0.00 0.00 3.01
2287 2409 1.446272 GAGGGGCTTGAAGACGACG 60.446 63.158 0.00 0.00 0.00 5.12
2300 2422 2.507102 CGACGCTTGCACTCCGAT 60.507 61.111 6.81 0.00 0.00 4.18
2326 2448 2.885135 AAATCCAGTGCCTGATGTCA 57.115 45.000 4.00 0.00 32.44 3.58
2355 2477 0.885879 CTCAGCTGCCAGCATTTTCA 59.114 50.000 20.53 0.00 45.56 2.69
2430 2552 1.474879 GATAGCAGCTCGGATAGGGAC 59.525 57.143 0.00 0.00 0.00 4.46
2490 2612 0.039764 TCGGTGAGGTGATGAGGAGT 59.960 55.000 0.00 0.00 0.00 3.85
2613 2735 2.928801 TGGGATCACCATTACCATCG 57.071 50.000 0.00 0.00 46.80 3.84
2655 2777 2.987232 GGTAACAAGAGGATGTCACCC 58.013 52.381 0.00 0.00 35.84 4.61
2719 2847 6.071784 TGTGATTTCTTTTGATGCTGCTGTAT 60.072 34.615 0.00 0.00 0.00 2.29
2799 2927 1.413118 ATGGCCGGGGAAATCATTTC 58.587 50.000 2.18 0.97 38.94 2.17
2820 2948 4.326826 TCAGGCAAGTTAGTGAAATCCAG 58.673 43.478 0.00 0.00 0.00 3.86
2835 2963 2.365586 CCAGGAGGAGCCAGAGGTG 61.366 68.421 0.00 0.00 40.02 4.00
2865 2993 2.613026 CATGCCAACATGCCATGAAT 57.387 45.000 12.53 0.00 46.75 2.57
2883 3011 8.420497 CCATGAATGGTGATTTGGACCACAAA 62.420 42.308 0.00 0.00 46.30 2.83
2928 3056 0.967380 AAGGGGAATTTCGGCTGCTG 60.967 55.000 0.95 0.95 0.00 4.41
3036 3164 2.622942 GGTTTCATTCAACACTGAGGCA 59.377 45.455 0.00 0.00 31.69 4.75
3222 3350 0.550914 TGGGGCTCAACAGAACAACT 59.449 50.000 0.00 0.00 0.00 3.16
3387 3515 1.251251 ATCTGAAGCAAAGTGGTGGC 58.749 50.000 0.00 0.00 0.00 5.01
3489 3617 9.277783 CATATAAAGATAGACCCAAACCAGAAG 57.722 37.037 0.00 0.00 0.00 2.85
4131 4261 5.596836 TGCCAACCTTTGATAATCAATCC 57.403 39.130 0.00 0.00 36.11 3.01
4189 4319 2.221169 TCACAACTGAGAATGGTGTGC 58.779 47.619 7.00 0.00 0.00 4.57
4233 4363 7.725844 ACTTCCACTTTGATTTTATTCCAGTCT 59.274 33.333 0.00 0.00 0.00 3.24
4251 4381 5.527214 CCAGTCTGTCTGTTCAACATGTTTA 59.473 40.000 8.77 0.00 42.19 2.01
4289 4419 6.089249 AGAACCATTCAGTTGGATTTGAAC 57.911 37.500 0.00 0.00 39.25 3.18
4295 4425 6.421801 CCATTCAGTTGGATTTGAACTGTTTC 59.578 38.462 11.34 0.00 46.94 2.78
4359 4489 9.546428 CATGAATTGTCTCAGTGTGGTATTATA 57.454 33.333 0.00 0.00 0.00 0.98
4382 4512 4.018870 ACAATTTCAACCCCCTTTTTGTGT 60.019 37.500 0.00 0.00 0.00 3.72
4389 4519 6.078664 TCAACCCCCTTTTTGTGTATGTTAT 58.921 36.000 0.00 0.00 0.00 1.89
4420 4550 8.908786 TTTGGCAGGATTACTAATAATCTGAG 57.091 34.615 4.10 0.00 44.29 3.35
4434 4564 7.565323 AATAATCTGAGACTTGATTGCCTTC 57.435 36.000 12.21 0.00 35.01 3.46
4480 4612 3.480470 AGGAACCAGTCACTGATTGTTG 58.520 45.455 6.30 0.00 32.44 3.33
4533 4665 9.669353 CCTAGCATTGAAACATAACATTATCAC 57.331 33.333 0.00 0.00 0.00 3.06
4537 4669 8.895845 GCATTGAAACATAACATTATCACGATC 58.104 33.333 0.00 0.00 0.00 3.69
4555 4687 1.734477 CGTTGTCTCAGTGGGCTCG 60.734 63.158 0.00 0.00 0.00 5.03
4712 4844 4.878397 TCCAATTTTGACGGTGCAATTTTT 59.122 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.249189 TCCCTGGGGCTCACACAC 61.249 66.667 14.00 0.00 34.68 3.82
1 2 3.249189 GTCCCTGGGGCTCACACA 61.249 66.667 10.89 0.00 34.68 3.72
2 3 3.249189 TGTCCCTGGGGCTCACAC 61.249 66.667 19.84 5.95 34.68 3.82
3 4 2.930019 CTGTCCCTGGGGCTCACA 60.930 66.667 19.84 11.67 34.68 3.58
4 5 3.721706 CCTGTCCCTGGGGCTCAC 61.722 72.222 19.84 7.13 34.68 3.51
6 7 4.741239 TCCCTGTCCCTGGGGCTC 62.741 72.222 19.84 7.64 42.03 4.70
7 8 4.748798 CTCCCTGTCCCTGGGGCT 62.749 72.222 19.84 0.00 42.03 5.19
10 11 2.080336 TTTTGCTCCCTGTCCCTGGG 62.080 60.000 6.33 6.33 42.93 4.45
11 12 0.178964 TTTTTGCTCCCTGTCCCTGG 60.179 55.000 0.00 0.00 0.00 4.45
12 13 0.961753 GTTTTTGCTCCCTGTCCCTG 59.038 55.000 0.00 0.00 0.00 4.45
13 14 0.853530 AGTTTTTGCTCCCTGTCCCT 59.146 50.000 0.00 0.00 0.00 4.20
14 15 2.557056 GTTAGTTTTTGCTCCCTGTCCC 59.443 50.000 0.00 0.00 0.00 4.46
15 16 3.219281 TGTTAGTTTTTGCTCCCTGTCC 58.781 45.455 0.00 0.00 0.00 4.02
16 17 4.261614 CCTTGTTAGTTTTTGCTCCCTGTC 60.262 45.833 0.00 0.00 0.00 3.51
17 18 3.636764 CCTTGTTAGTTTTTGCTCCCTGT 59.363 43.478 0.00 0.00 0.00 4.00
169 175 1.672356 GCCTCGCTTTGGAGCTGAA 60.672 57.895 0.00 0.00 46.96 3.02
170 176 2.046892 GCCTCGCTTTGGAGCTGA 60.047 61.111 0.00 0.00 46.96 4.26
198 209 1.546029 TCACTACCACTACTGCTGCTG 59.454 52.381 4.89 4.89 0.00 4.41
201 212 2.558795 ACACTCACTACCACTACTGCTG 59.441 50.000 0.00 0.00 0.00 4.41
204 215 5.936372 TGTACTACACTCACTACCACTACTG 59.064 44.000 0.00 0.00 0.00 2.74
205 216 6.119240 TGTACTACACTCACTACCACTACT 57.881 41.667 0.00 0.00 0.00 2.57
206 217 6.808008 TTGTACTACACTCACTACCACTAC 57.192 41.667 0.00 0.00 0.00 2.73
207 218 6.772233 TGTTTGTACTACACTCACTACCACTA 59.228 38.462 0.00 0.00 0.00 2.74
208 219 5.595542 TGTTTGTACTACACTCACTACCACT 59.404 40.000 0.00 0.00 0.00 4.00
209 220 5.835257 TGTTTGTACTACACTCACTACCAC 58.165 41.667 0.00 0.00 0.00 4.16
210 221 5.010314 CCTGTTTGTACTACACTCACTACCA 59.990 44.000 0.00 0.00 0.00 3.25
212 223 5.467705 CCCTGTTTGTACTACACTCACTAC 58.532 45.833 0.00 0.00 0.00 2.73
214 225 3.323979 CCCCTGTTTGTACTACACTCACT 59.676 47.826 0.00 0.00 0.00 3.41
381 406 3.072915 TGGAAATCTCAAGAGCAAGGTCA 59.927 43.478 1.84 0.00 0.00 4.02
382 407 3.438434 GTGGAAATCTCAAGAGCAAGGTC 59.562 47.826 0.00 0.00 0.00 3.85
383 408 3.073650 AGTGGAAATCTCAAGAGCAAGGT 59.926 43.478 0.00 0.00 0.00 3.50
395 479 4.805609 GCTCTCTCAAACCAGTGGAAATCT 60.806 45.833 18.40 0.00 0.00 2.40
420 506 3.499918 CACCACCAAGAAGAACTCATCAC 59.500 47.826 0.00 0.00 0.00 3.06
495 581 8.856153 AAGAAGAGGGATAGAAAGAAAGAAAC 57.144 34.615 0.00 0.00 0.00 2.78
610 709 1.624312 GAGAAGAAACGGAGGAGGGTT 59.376 52.381 0.00 0.00 0.00 4.11
631 730 0.459585 CCGCGGATTTTCTCGGAGAA 60.460 55.000 24.07 16.19 44.23 2.87
735 852 3.887716 GAGAATGGGGGATCAGAAATGTG 59.112 47.826 0.00 0.00 0.00 3.21
942 1060 4.700365 GAAACCAACCGCAGCGCC 62.700 66.667 10.07 0.00 0.00 6.53
955 1073 2.046604 CGACGGGGAAGGGGAAAC 60.047 66.667 0.00 0.00 0.00 2.78
956 1074 2.527374 ACGACGGGGAAGGGGAAA 60.527 61.111 0.00 0.00 0.00 3.13
957 1075 2.999063 GACGACGGGGAAGGGGAA 60.999 66.667 0.00 0.00 0.00 3.97
960 1078 3.135056 GATCGACGACGGGGAAGGG 62.135 68.421 7.55 0.00 40.21 3.95
961 1079 2.412112 GATCGACGACGGGGAAGG 59.588 66.667 7.55 0.00 40.21 3.46
962 1080 2.412112 GGATCGACGACGGGGAAG 59.588 66.667 7.55 0.00 40.21 3.46
1383 1502 2.753043 GTGGAGGCGTAGTCCGGA 60.753 66.667 0.00 0.00 36.82 5.14
1471 1590 1.080093 CGAAGCCGCAGTAGTCCAA 60.080 57.895 0.00 0.00 0.00 3.53
1473 1592 2.202756 CCGAAGCCGCAGTAGTCC 60.203 66.667 0.00 0.00 0.00 3.85
1523 1645 1.350193 CTCGGACAATGTGAAGGACG 58.650 55.000 0.00 0.00 0.00 4.79
1524 1646 1.079503 GCTCGGACAATGTGAAGGAC 58.920 55.000 0.00 0.00 0.00 3.85
1525 1647 0.976641 AGCTCGGACAATGTGAAGGA 59.023 50.000 0.00 0.00 0.00 3.36
1599 1721 2.208431 CGCTCCTTGATGTCATTCTCC 58.792 52.381 0.00 0.00 0.00 3.71
1626 1748 0.999406 CCGGCACATTCAAGTACTCG 59.001 55.000 0.00 0.00 0.00 4.18
1716 1838 1.002087 AGCCTTCGGTTGTTCTCGAAT 59.998 47.619 0.00 0.00 43.13 3.34
2073 2195 8.361139 CGGTAGAATGAGGTTATAATGAAGTCT 58.639 37.037 0.00 0.00 0.00 3.24
2098 2220 2.327228 GGTCAGAACCAAACACCCG 58.673 57.895 0.00 0.00 45.68 5.28
2151 2273 1.341383 CCCTGCAAGCTCCCAATAACT 60.341 52.381 0.00 0.00 0.00 2.24
2160 2282 0.750911 CATTCCTCCCCTGCAAGCTC 60.751 60.000 0.00 0.00 0.00 4.09
2202 2324 4.349636 TGTGGAAAGACTGGAACAATCCTA 59.650 41.667 0.00 0.00 46.70 2.94
2268 2390 1.079057 GTCGTCTTCAAGCCCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2274 2396 1.154580 GCAAGCGTCGTCTTCAAGC 60.155 57.895 0.00 0.00 0.00 4.01
2283 2405 1.202973 CTATCGGAGTGCAAGCGTCG 61.203 60.000 0.00 0.00 0.00 5.12
2287 2409 2.515926 TCATCTATCGGAGTGCAAGC 57.484 50.000 0.00 0.00 0.00 4.01
2326 2448 1.224039 GCAGCTGAGAGCCATTCCT 59.776 57.895 20.43 0.00 43.77 3.36
2337 2459 0.885879 CTGAAAATGCTGGCAGCTGA 59.114 50.000 36.50 20.85 42.97 4.26
2355 2477 0.314302 GAGCAGACGTGTACACACCT 59.686 55.000 24.98 17.19 43.66 4.00
2367 2489 1.472480 GTCTCTCTGACCTGAGCAGAC 59.528 57.143 0.00 14.16 39.69 3.51
2412 2534 0.889638 CGTCCCTATCCGAGCTGCTA 60.890 60.000 0.15 0.00 0.00 3.49
2430 2552 2.635443 AAAAATGGTGCTCGCCCCG 61.635 57.895 0.00 0.00 0.00 5.73
2490 2612 1.219124 GTCCTCGCTGAATGCTGGA 59.781 57.895 0.00 0.00 38.78 3.86
2613 2735 1.967319 TTCTGCCAGTGAACCAAGAC 58.033 50.000 0.00 0.00 0.00 3.01
2655 2777 5.012458 TGGGCTTCTAGATATCCTTGATGTG 59.988 44.000 0.00 0.00 0.00 3.21
2661 2789 7.514127 TCATAAAGTGGGCTTCTAGATATCCTT 59.486 37.037 0.00 0.00 33.01 3.36
2719 2847 6.479990 CAGTCTACATCTTGTGAAACTGACAA 59.520 38.462 10.71 0.00 37.34 3.18
2799 2927 3.441572 CCTGGATTTCACTAACTTGCCTG 59.558 47.826 0.00 0.00 0.00 4.85
2820 2948 1.613630 TTCCACCTCTGGCTCCTCC 60.614 63.158 0.00 0.00 37.49 4.30
2835 2963 0.244721 GTTGGCATGCAACCTCTTCC 59.755 55.000 21.36 0.00 0.00 3.46
2865 2993 3.304911 TCTTTGTGGTCCAAATCACCA 57.695 42.857 0.00 0.00 42.02 4.17
2883 3011 3.769844 TCTCCCTTCTTATCGCACTTTCT 59.230 43.478 0.00 0.00 0.00 2.52
2928 3056 1.223763 GTTTCCATCCCTCCGTCCC 59.776 63.158 0.00 0.00 0.00 4.46
2961 3089 1.002250 CAACACCGAAGAGACGACCG 61.002 60.000 0.00 0.00 35.09 4.79
3015 3143 2.622942 TGCCTCAGTGTTGAATGAAACC 59.377 45.455 0.00 0.00 31.69 3.27
3036 3164 7.170489 CGATGTAGTCTGTCAGCAATCATATTT 59.830 37.037 0.00 0.00 0.00 1.40
3114 3242 7.279536 GCATCATCATACCCATCACTTATACAG 59.720 40.741 0.00 0.00 0.00 2.74
3387 3515 6.237648 GGACAAATTCAGCATTAATGAAAGCG 60.238 38.462 19.73 2.15 39.92 4.68
3489 3617 2.977914 TCTAGTGCTCCATTTGACTGC 58.022 47.619 0.00 0.00 0.00 4.40
3730 3858 3.389925 TCAAGCTCAAATTTGCCCTTG 57.610 42.857 27.23 27.23 37.35 3.61
3949 4077 7.064016 GCTTTACAAACATTGTTCAGTGGAAAA 59.936 33.333 14.37 8.80 42.22 2.29
4113 4243 7.043565 GCAACATGGATTGATTATCAAAGGTT 58.956 34.615 11.88 6.98 40.12 3.50
4131 4261 1.741706 GGACAGTCATCCAGCAACATG 59.258 52.381 2.17 0.00 38.77 3.21
4189 4319 2.314647 TTGGAACTTCGAAGCGGCG 61.315 57.895 24.86 0.51 0.00 6.46
4233 4363 7.066887 ACAAGACATAAACATGTTGAACAGACA 59.933 33.333 12.82 0.00 34.45 3.41
4251 4381 8.408043 TGAATGGTTCTATTTCAACAAGACAT 57.592 30.769 0.00 0.00 0.00 3.06
4289 4419 7.259161 AGGAAAGCGATAGTACTTAGAAACAG 58.741 38.462 0.00 0.00 39.35 3.16
4295 4425 6.697892 CCAAGAAGGAAAGCGATAGTACTTAG 59.302 42.308 0.00 0.00 41.22 2.18
4307 4437 2.587522 AGTTCACCCAAGAAGGAAAGC 58.412 47.619 0.00 0.00 41.22 3.51
4359 4489 4.018870 ACACAAAAAGGGGGTTGAAATTGT 60.019 37.500 0.00 0.00 0.00 2.71
4420 4550 4.034510 CAGGTTATCGAAGGCAATCAAGTC 59.965 45.833 0.00 0.00 0.00 3.01
4427 4557 3.450817 TCAGATCAGGTTATCGAAGGCAA 59.549 43.478 0.00 0.00 0.00 4.52
4434 4564 4.686972 TGCTTCTTCAGATCAGGTTATCG 58.313 43.478 0.00 0.00 0.00 2.92
4533 4665 1.078759 GCCCACTGAGACAACGATCG 61.079 60.000 14.88 14.88 0.00 3.69
4537 4669 1.734477 CGAGCCCACTGAGACAACG 60.734 63.158 0.00 0.00 0.00 4.10
4555 4687 8.798859 ATGGTTATACAGGATCTTATTCATGC 57.201 34.615 0.00 0.00 30.75 4.06


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

AutoCloner maintained by Alex Coulton.