Multiple sequence alignment - TraesCS1A01G184500

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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 TraesCS1A01G184500 chr1A 100.000 4901 0 0 1 4901 334453553 334448653 0.000000e+00 9051.0
1 TraesCS1A01G184500 chr1A 95.975 472 14 3 4271 4737 334416718 334416247 0.000000e+00 761.0
2 TraesCS1A01G184500 chr1D 94.390 4902 188 40 1 4863 267984935 267989788 0.000000e+00 7448.0
3 TraesCS1A01G184500 chr1D 88.250 400 37 5 4222 4618 268461813 268462205 2.070000e-128 470.0
4 TraesCS1A01G184500 chr1D 95.370 108 3 2 4614 4719 268467360 268467467 2.350000e-38 171.0
5 TraesCS1A01G184500 chr1B 94.518 2955 124 18 1830 4772 344841081 344838153 0.000000e+00 4525.0
6 TraesCS1A01G184500 chr1B 94.050 1042 38 12 712 1747 344842218 344841195 0.000000e+00 1559.0
7 TraesCS1A01G184500 chr1B 93.651 252 12 3 460 707 344842518 344842267 1.670000e-99 374.0
8 TraesCS1A01G184500 chr1B 89.024 82 8 1 2429 2509 344840409 344840328 3.120000e-17 100.0
9 TraesCS1A01G184500 chr1B 80.137 146 18 9 99 237 221132018 221131877 1.120000e-16 99.0
10 TraesCS1A01G184500 chr2B 85.897 156 21 1 110 265 752925204 752925050 1.090000e-36 165.0
11 TraesCS1A01G184500 chr6D 75.758 165 34 6 104 265 57999645 57999806 1.460000e-10 78.7
12 TraesCS1A01G184500 chr5B 89.474 57 6 0 209 265 50467958 50468014 6.800000e-09 73.1
13 TraesCS1A01G184500 chr4A 89.091 55 6 0 211 265 37058775 37058829 8.800000e-08 69.4
14 TraesCS1A01G184500 chr4A 90.385 52 5 0 209 260 90082019 90082070 8.800000e-08 69.4
15 TraesCS1A01G184500 chr4B 91.667 48 4 0 206 253 541919530 541919577 3.170000e-07 67.6
16 TraesCS1A01G184500 chr3D 87.719 57 7 0 210 266 83935271 83935215 3.170000e-07 67.6
17 TraesCS1A01G184500 chr3D 92.857 42 3 0 228 269 389213934 389213893 1.470000e-05 62.1


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 TraesCS1A01G184500 chr1A 334448653 334453553 4900 True 9051.0 9051 100.00000 1 4901 1 chr1A.!!$R2 4900
1 TraesCS1A01G184500 chr1D 267984935 267989788 4853 False 7448.0 7448 94.39000 1 4863 1 chr1D.!!$F1 4862
2 TraesCS1A01G184500 chr1B 344838153 344842518 4365 True 1639.5 4525 92.81075 460 4772 4 chr1B.!!$R2 4312

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
893 949 1.066502 GGAAGCTTCTCCACCAGAGTC 60.067 57.143 25.05 0.96 43.71 3.36 F
1184 1242 1.237285 GGCATTGTCTGGTGCGTTCT 61.237 55.000 0.00 0.00 42.15 3.01 F
1198 1257 1.327690 CGTTCTCCCCTCCCGAATCA 61.328 60.000 0.00 0.00 0.00 2.57 F
2345 2435 0.315251 GGTTTGTTGCCTCCTGCTTC 59.685 55.000 0.00 0.00 42.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1929 1.054406 TGGGTAGGGCCATACTCTGC 61.054 60.000 26.72 10.63 39.65 4.26 R
2101 2190 1.963515 GAGTGGACAACAAAGCCCATT 59.036 47.619 0.00 0.00 0.00 3.16 R
3012 3102 4.567971 AGCTCAGAAACAGACTCATCTTG 58.432 43.478 0.00 0.00 30.42 3.02 R
4200 4293 0.670546 ACAACGGAGAATCGGCACAG 60.671 55.000 0.00 0.00 39.30 3.66 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
88 89 4.346730 TCATGCATGAAAGAAGACCCATT 58.653 39.130 26.87 0.00 33.08 3.16
109 110 7.257722 CCATTACATTCAATTCTTGTACACCC 58.742 38.462 0.00 0.00 0.00 4.61
125 126 4.684484 ACACCCTCCGTTCCTAAATATC 57.316 45.455 0.00 0.00 0.00 1.63
126 127 4.035112 ACACCCTCCGTTCCTAAATATCA 58.965 43.478 0.00 0.00 0.00 2.15
127 128 4.101119 ACACCCTCCGTTCCTAAATATCAG 59.899 45.833 0.00 0.00 0.00 2.90
128 129 4.344102 CACCCTCCGTTCCTAAATATCAGA 59.656 45.833 0.00 0.00 0.00 3.27
129 130 4.344390 ACCCTCCGTTCCTAAATATCAGAC 59.656 45.833 0.00 0.00 0.00 3.51
130 131 4.344102 CCCTCCGTTCCTAAATATCAGACA 59.656 45.833 0.00 0.00 0.00 3.41
131 132 5.012148 CCCTCCGTTCCTAAATATCAGACAT 59.988 44.000 0.00 0.00 0.00 3.06
132 133 6.464465 CCCTCCGTTCCTAAATATCAGACATT 60.464 42.308 0.00 0.00 0.00 2.71
133 134 6.992715 CCTCCGTTCCTAAATATCAGACATTT 59.007 38.462 0.00 0.00 0.00 2.32
134 135 7.499232 CCTCCGTTCCTAAATATCAGACATTTT 59.501 37.037 0.00 0.00 0.00 1.82
135 136 9.542462 CTCCGTTCCTAAATATCAGACATTTTA 57.458 33.333 0.00 0.00 0.00 1.52
136 137 9.893634 TCCGTTCCTAAATATCAGACATTTTAA 57.106 29.630 0.00 0.00 0.00 1.52
173 174 7.407729 TGGGACTACATACGGATGAATATAGA 58.592 38.462 16.36 0.00 36.48 1.98
176 177 8.182881 GGACTACATACGGATGAATATAGACAC 58.817 40.741 16.36 3.55 36.48 3.67
185 186 9.698309 ACGGATGAATATAGACACATTTTAGAG 57.302 33.333 0.00 0.00 0.00 2.43
206 207 6.112058 AGAGTTAGATTCACTCATTTGGCTC 58.888 40.000 6.85 0.00 42.85 4.70
207 208 6.059787 AGTTAGATTCACTCATTTGGCTCT 57.940 37.500 0.00 0.00 0.00 4.09
208 209 7.124901 AGAGTTAGATTCACTCATTTGGCTCTA 59.875 37.037 6.85 0.00 42.85 2.43
270 271 6.569179 TTAAAAACAGAGGGAGTAACATGC 57.431 37.500 0.00 0.00 0.00 4.06
272 273 3.788227 AACAGAGGGAGTAACATGCAA 57.212 42.857 0.00 0.00 0.00 4.08
273 274 4.307032 AACAGAGGGAGTAACATGCAAT 57.693 40.909 0.00 0.00 0.00 3.56
289 290 6.763303 CATGCAATCATGTAATTCACCATG 57.237 37.500 0.00 6.41 43.85 3.66
614 618 8.067784 CGTCTTTGCAGTTTCTTACAATAAAGA 58.932 33.333 0.00 0.00 33.02 2.52
622 626 9.231297 CAGTTTCTTACAATAAAGAATGGAGGA 57.769 33.333 0.29 0.00 43.21 3.71
623 627 9.454859 AGTTTCTTACAATAAAGAATGGAGGAG 57.545 33.333 0.29 0.00 43.21 3.69
624 628 9.232473 GTTTCTTACAATAAAGAATGGAGGAGT 57.768 33.333 0.29 0.00 43.21 3.85
627 631 9.488762 TCTTACAATAAAGAATGGAGGAGTAGA 57.511 33.333 0.00 0.00 32.59 2.59
630 634 8.324191 ACAATAAAGAATGGAGGAGTAGATCA 57.676 34.615 0.00 0.00 0.00 2.92
637 642 7.129425 AGAATGGAGGAGTAGATCAGTAAAGT 58.871 38.462 0.00 0.00 0.00 2.66
697 704 3.418684 AAGGTGTGTATGAACCCTCAC 57.581 47.619 0.00 0.00 37.13 3.51
704 711 4.764823 TGTGTATGAACCCTCACCATTTTC 59.235 41.667 0.00 0.00 33.30 2.29
705 712 5.010282 GTGTATGAACCCTCACCATTTTCT 58.990 41.667 0.00 0.00 33.30 2.52
707 714 6.657541 GTGTATGAACCCTCACCATTTTCTTA 59.342 38.462 0.00 0.00 33.30 2.10
708 715 7.175990 GTGTATGAACCCTCACCATTTTCTTAA 59.824 37.037 0.00 0.00 33.30 1.85
709 716 7.726291 TGTATGAACCCTCACCATTTTCTTAAA 59.274 33.333 0.00 0.00 33.30 1.52
743 795 9.545611 CAAAGCAATAAATTAAGCAAATTGGAC 57.454 29.630 0.00 0.00 37.85 4.02
893 949 1.066502 GGAAGCTTCTCCACCAGAGTC 60.067 57.143 25.05 0.96 43.71 3.36
1134 1192 4.832608 GCCTCCAAGTACGCCCCG 62.833 72.222 0.00 0.00 0.00 5.73
1184 1242 1.237285 GGCATTGTCTGGTGCGTTCT 61.237 55.000 0.00 0.00 42.15 3.01
1198 1257 1.327690 CGTTCTCCCCTCCCGAATCA 61.328 60.000 0.00 0.00 0.00 2.57
1275 1334 3.138304 TGCCATGTGTAGAATATTCCGC 58.862 45.455 11.92 5.24 0.00 5.54
1328 1387 2.095466 CACATGCGGGTATGACGTTTTT 60.095 45.455 3.72 0.00 0.00 1.94
1609 1668 4.340950 TGGACATGTATAGTGATTGCTCGA 59.659 41.667 0.00 0.00 0.00 4.04
1620 1679 2.279741 GATTGCTCGATGTACTTGCCA 58.720 47.619 0.00 0.00 0.00 4.92
1646 1705 3.492313 GCTATAAGTGTTTGCTGTGTGC 58.508 45.455 0.00 0.00 43.25 4.57
1848 1937 7.792374 ATGTTGAATGTAAATCGCAGAGTAT 57.208 32.000 0.00 0.00 43.63 2.12
1901 1990 8.615211 TGCTTGATTATGTACATGATGAAGTTC 58.385 33.333 28.03 18.61 33.08 3.01
2008 2097 5.514279 CGCTGACAATTTTCTCTGAAGTTT 58.486 37.500 0.00 0.00 0.00 2.66
2053 2142 5.063880 TCCTTTGTCCAAGTTTCTAGAAGC 58.936 41.667 11.09 11.09 0.00 3.86
2162 2252 8.506083 AGTCATTCCTATGATGGGTTTATTCTT 58.494 33.333 0.00 0.00 42.49 2.52
2272 2362 4.681074 TGTTACTGAGTTGATGGACACA 57.319 40.909 0.00 0.00 0.00 3.72
2345 2435 0.315251 GGTTTGTTGCCTCCTGCTTC 59.685 55.000 0.00 0.00 42.00 3.86
2371 2461 5.689068 GCCAAGATTCTTATGTATTTGCTGC 59.311 40.000 0.00 0.00 0.00 5.25
2377 2467 6.890663 TTCTTATGTATTTGCTGCAATTGC 57.109 33.333 23.69 23.69 42.50 3.56
2394 2484 6.131389 GCAATTGCAGTTGAAACAAATCTTC 58.869 36.000 25.36 0.00 41.59 2.87
2396 2486 7.342194 CAATTGCAGTTGAAACAAATCTTCTG 58.658 34.615 16.35 0.00 0.00 3.02
2433 2523 7.716612 AGATATCGATTGACATGTACTCACAA 58.283 34.615 1.71 0.00 38.42 3.33
2443 2533 6.542005 TGACATGTACTCACAATTGTGTTCTT 59.458 34.615 31.99 19.13 45.76 2.52
2444 2534 6.959361 ACATGTACTCACAATTGTGTTCTTC 58.041 36.000 31.99 20.89 45.76 2.87
2445 2535 6.542005 ACATGTACTCACAATTGTGTTCTTCA 59.458 34.615 31.99 24.48 45.76 3.02
2515 2605 9.341899 GAAATCATAAGTTACATGTTGTGTTCC 57.658 33.333 2.30 0.00 42.29 3.62
2945 3035 4.341806 TGAGGTAGGTTTGTTCAACTCGTA 59.658 41.667 0.00 0.00 35.46 3.43
3012 3102 7.148188 TGTCTATTTGGAAGCTGTCAATCAATC 60.148 37.037 3.30 0.00 0.00 2.67
3126 3216 6.822442 TGACTGTATTGTTAGACCTGTTTCA 58.178 36.000 0.00 0.00 0.00 2.69
3228 3318 3.052036 GGTGCTGCAACATTTTACTGTG 58.948 45.455 13.80 0.00 0.00 3.66
3343 3433 3.957497 ACTGGTTGGTTTCTGTGCAATAA 59.043 39.130 0.00 0.00 0.00 1.40
3368 3458 6.422776 TTCTTAGCTTCAAATCGACCATTC 57.577 37.500 0.00 0.00 0.00 2.67
3379 3470 3.770263 TCGACCATTCTTAGTACCACG 57.230 47.619 0.00 0.00 0.00 4.94
3428 3519 4.129380 TGATGTCTCTTGAACCTGTTGTG 58.871 43.478 0.00 0.00 0.00 3.33
3470 3561 1.338020 CCGGCTTTCTGCTTCAAAAGT 59.662 47.619 0.00 0.00 42.39 2.66
3795 3886 1.228124 CGAAGAACCCACTTGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
3980 4071 9.166173 CCAATTATCTAGAAGAACACAATGTGA 57.834 33.333 21.34 0.00 36.96 3.58
4001 4092 7.220740 TGTGATCAGACGACTAATCTAGATCT 58.779 38.462 5.51 0.00 34.84 2.75
4006 4097 6.483974 TCAGACGACTAATCTAGATCTTGGAC 59.516 42.308 5.51 0.00 0.00 4.02
4007 4098 5.467399 AGACGACTAATCTAGATCTTGGACG 59.533 44.000 5.51 8.91 0.00 4.79
4025 4118 1.825474 ACGTGAGGAGGTTCATACAGG 59.175 52.381 0.00 0.00 0.00 4.00
4158 4251 7.286775 AGTTTGAGAACATACCCTGCTTAAAAA 59.713 33.333 0.00 0.00 38.26 1.94
4190 4283 7.639113 TGTAAGTCAAGTCTTGTTTTTCCAT 57.361 32.000 12.30 0.00 0.00 3.41
4200 4293 7.035612 AGTCTTGTTTTTCCATGTTTCTTGTC 58.964 34.615 0.00 0.00 0.00 3.18
4207 4302 1.069022 CCATGTTTCTTGTCTGTGCCG 60.069 52.381 0.00 0.00 0.00 5.69
4214 4309 1.066858 TCTTGTCTGTGCCGATTCTCC 60.067 52.381 0.00 0.00 0.00 3.71
4383 4478 5.221106 CCGATATTTCCATGTCTTGTGCATT 60.221 40.000 0.00 0.00 0.00 3.56
4505 4600 4.047059 CTTGCGCCTGGGCTTGTG 62.047 66.667 4.18 0.00 39.32 3.33
4558 4654 8.946085 TCTTGTGTATCTAAGGCTTGTAATTTG 58.054 33.333 10.69 0.00 0.00 2.32
4559 4655 8.630054 TTGTGTATCTAAGGCTTGTAATTTGT 57.370 30.769 10.69 0.00 0.00 2.83
4560 4656 8.263940 TGTGTATCTAAGGCTTGTAATTTGTC 57.736 34.615 10.69 0.00 0.00 3.18
4720 4820 4.698780 GGTGTATCCCACAGTAAAAGTTCC 59.301 45.833 0.00 0.00 46.44 3.62
4734 4834 8.607459 CAGTAAAAGTTCCTACATGCTATTCTG 58.393 37.037 0.00 0.00 0.00 3.02
4756 4856 5.345702 TGCGCACTAGTACTTGGTTATTAG 58.654 41.667 5.66 0.00 0.00 1.73
4800 4905 0.460109 CATGAACGCATGGTCGAGGA 60.460 55.000 0.00 0.00 46.45 3.71
4801 4906 0.179100 ATGAACGCATGGTCGAGGAG 60.179 55.000 0.00 0.00 32.31 3.69
4811 4916 4.822026 CATGGTCGAGGAGTAGAAAGTTT 58.178 43.478 0.00 0.00 0.00 2.66
4816 4921 4.863689 GTCGAGGAGTAGAAAGTTTTAGCC 59.136 45.833 0.00 0.00 0.00 3.93
4819 4924 5.336531 CGAGGAGTAGAAAGTTTTAGCCTCA 60.337 44.000 16.85 0.00 39.39 3.86
4863 4968 0.674895 AGCTCAAGCCATTCACCGTC 60.675 55.000 0.00 0.00 43.38 4.79
4864 4969 1.648467 GCTCAAGCCATTCACCGTCC 61.648 60.000 0.00 0.00 34.31 4.79
4865 4970 0.321564 CTCAAGCCATTCACCGTCCA 60.322 55.000 0.00 0.00 0.00 4.02
4866 4971 0.605319 TCAAGCCATTCACCGTCCAC 60.605 55.000 0.00 0.00 0.00 4.02
4867 4972 1.671054 AAGCCATTCACCGTCCACG 60.671 57.895 0.00 0.00 39.44 4.94
4888 4993 4.457496 CAGTGAGCCCGCCGACAT 62.457 66.667 0.00 0.00 0.00 3.06
4889 4994 3.706373 AGTGAGCCCGCCGACATT 61.706 61.111 0.00 0.00 0.00 2.71
4890 4995 3.499737 GTGAGCCCGCCGACATTG 61.500 66.667 0.00 0.00 0.00 2.82
4891 4996 4.015406 TGAGCCCGCCGACATTGT 62.015 61.111 0.00 0.00 0.00 2.71
4892 4997 2.746277 GAGCCCGCCGACATTGTT 60.746 61.111 0.00 0.00 0.00 2.83
4893 4998 3.039202 GAGCCCGCCGACATTGTTG 62.039 63.158 0.00 0.00 0.00 3.33
4894 4999 4.776647 GCCCGCCGACATTGTTGC 62.777 66.667 0.00 0.80 0.00 4.17
4895 5000 3.361158 CCCGCCGACATTGTTGCA 61.361 61.111 11.32 0.00 0.00 4.08
4896 5001 2.126888 CCGCCGACATTGTTGCAC 60.127 61.111 11.32 0.72 0.00 4.57
4897 5002 2.636462 CGCCGACATTGTTGCACA 59.364 55.556 11.32 0.00 0.00 4.57
4898 5003 1.209898 CGCCGACATTGTTGCACAT 59.790 52.632 11.32 0.00 0.00 3.21
4899 5004 1.066656 CGCCGACATTGTTGCACATG 61.067 55.000 11.32 0.00 0.00 3.21
4900 5005 0.240678 GCCGACATTGTTGCACATGA 59.759 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.638421 GGGCTAACATAGTTGCATGTTACA 59.362 41.667 6.54 0.00 45.13 2.41
109 110 8.438676 AAAATGTCTGATATTTAGGAACGGAG 57.561 34.615 11.95 0.00 0.00 4.63
136 137 9.720769 CCGTATGTAGTCCCATATTTAAATCTT 57.279 33.333 3.39 0.00 30.47 2.40
137 138 9.096823 TCCGTATGTAGTCCCATATTTAAATCT 57.903 33.333 3.39 0.00 30.47 2.40
138 139 9.886132 ATCCGTATGTAGTCCCATATTTAAATC 57.114 33.333 3.39 0.00 30.47 2.17
139 140 9.667107 CATCCGTATGTAGTCCCATATTTAAAT 57.333 33.333 5.89 5.89 30.47 1.40
140 141 8.872134 TCATCCGTATGTAGTCCCATATTTAAA 58.128 33.333 0.00 0.00 34.50 1.52
141 142 8.425237 TCATCCGTATGTAGTCCCATATTTAA 57.575 34.615 0.00 0.00 34.50 1.52
142 143 8.425237 TTCATCCGTATGTAGTCCCATATTTA 57.575 34.615 0.00 0.00 34.50 1.40
143 144 6.928348 TCATCCGTATGTAGTCCCATATTT 57.072 37.500 0.00 0.00 34.50 1.40
144 145 6.928348 TTCATCCGTATGTAGTCCCATATT 57.072 37.500 0.00 0.00 34.50 1.28
145 146 8.783660 ATATTCATCCGTATGTAGTCCCATAT 57.216 34.615 0.00 0.00 34.50 1.78
146 147 9.350951 CTATATTCATCCGTATGTAGTCCCATA 57.649 37.037 0.00 0.00 34.50 2.74
147 148 8.059461 TCTATATTCATCCGTATGTAGTCCCAT 58.941 37.037 0.00 0.00 34.50 4.00
148 149 7.338703 GTCTATATTCATCCGTATGTAGTCCCA 59.661 40.741 0.00 0.00 34.50 4.37
149 150 7.338703 TGTCTATATTCATCCGTATGTAGTCCC 59.661 40.741 0.00 0.00 34.50 4.46
173 174 9.950496 ATGAGTGAATCTAACTCTAAAATGTGT 57.050 29.630 5.29 0.00 43.69 3.72
185 186 9.717942 ATATAGAGCCAAATGAGTGAATCTAAC 57.282 33.333 0.00 0.00 0.00 2.34
234 235 8.758829 CCCTCTGTTTTTAAATATAAGCCCTTT 58.241 33.333 0.00 0.00 0.00 3.11
248 249 5.626142 TGCATGTTACTCCCTCTGTTTTTA 58.374 37.500 0.00 0.00 0.00 1.52
249 250 4.469657 TGCATGTTACTCCCTCTGTTTTT 58.530 39.130 0.00 0.00 0.00 1.94
250 251 4.098914 TGCATGTTACTCCCTCTGTTTT 57.901 40.909 0.00 0.00 0.00 2.43
254 255 3.877559 TGATTGCATGTTACTCCCTCTG 58.122 45.455 0.00 0.00 0.00 3.35
255 256 4.458397 CATGATTGCATGTTACTCCCTCT 58.542 43.478 0.00 0.00 45.41 3.69
269 270 4.053295 GGCATGGTGAATTACATGATTGC 58.947 43.478 16.88 6.69 45.55 3.56
270 271 5.045215 GTGGCATGGTGAATTACATGATTG 58.955 41.667 16.88 0.00 45.55 2.67
272 273 3.638160 GGTGGCATGGTGAATTACATGAT 59.362 43.478 16.88 0.00 45.55 2.45
273 274 3.023119 GGTGGCATGGTGAATTACATGA 58.977 45.455 16.88 0.23 45.55 3.07
575 579 6.220930 ACTGCAAAGACGTCTTACATTAAGA 58.779 36.000 29.91 8.48 42.19 2.10
614 618 6.039941 CGACTTTACTGATCTACTCCTCCATT 59.960 42.308 0.00 0.00 0.00 3.16
622 626 6.598457 TGCTCTAACGACTTTACTGATCTACT 59.402 38.462 0.00 0.00 0.00 2.57
623 627 6.783162 TGCTCTAACGACTTTACTGATCTAC 58.217 40.000 0.00 0.00 0.00 2.59
624 628 6.997239 TGCTCTAACGACTTTACTGATCTA 57.003 37.500 0.00 0.00 0.00 1.98
625 629 5.899120 TGCTCTAACGACTTTACTGATCT 57.101 39.130 0.00 0.00 0.00 2.75
626 630 8.804688 ATATTGCTCTAACGACTTTACTGATC 57.195 34.615 0.00 0.00 0.00 2.92
628 632 9.731819 CTTATATTGCTCTAACGACTTTACTGA 57.268 33.333 0.00 0.00 0.00 3.41
629 633 8.969267 CCTTATATTGCTCTAACGACTTTACTG 58.031 37.037 0.00 0.00 0.00 2.74
630 634 8.693625 ACCTTATATTGCTCTAACGACTTTACT 58.306 33.333 0.00 0.00 0.00 2.24
637 642 6.216801 ACACACCTTATATTGCTCTAACGA 57.783 37.500 0.00 0.00 0.00 3.85
708 715 9.586435 GCTTAATTTATTGCTTTGTACTCCATT 57.414 29.630 0.00 0.00 0.00 3.16
709 716 8.748412 TGCTTAATTTATTGCTTTGTACTCCAT 58.252 29.630 0.00 0.00 0.00 3.41
717 769 9.545611 GTCCAATTTGCTTAATTTATTGCTTTG 57.454 29.630 0.00 0.00 34.19 2.77
739 791 5.166013 AGGTAGATAGGGGTAAATGTCCA 57.834 43.478 0.00 0.00 0.00 4.02
770 826 3.303526 CGACGTTAAGGGGAAAACACAAG 60.304 47.826 0.00 0.00 0.00 3.16
772 828 2.211806 CGACGTTAAGGGGAAAACACA 58.788 47.619 0.00 0.00 0.00 3.72
773 829 1.069703 GCGACGTTAAGGGGAAAACAC 60.070 52.381 0.00 0.00 0.00 3.32
893 949 2.755469 CGTTCATGGGCTTGGGGG 60.755 66.667 0.00 0.00 0.00 5.40
1318 1377 8.952278 TCATAACTTTATGCCTAAAAACGTCAT 58.048 29.630 4.36 0.00 40.19 3.06
1328 1387 7.933577 CACTTCCTCATCATAACTTTATGCCTA 59.066 37.037 4.36 0.00 40.19 3.93
1609 1668 5.011738 ACTTATAGCGGTATGGCAAGTACAT 59.988 40.000 17.16 0.00 34.64 2.29
1620 1679 4.570772 CACAGCAAACACTTATAGCGGTAT 59.429 41.667 12.42 12.42 32.61 2.73
1703 1762 4.177026 ACTAATAAGAGCAGCGTTCACAG 58.823 43.478 0.00 0.00 0.00 3.66
1828 1917 4.511454 GCCATACTCTGCGATTTACATTCA 59.489 41.667 0.00 0.00 0.00 2.57
1840 1929 1.054406 TGGGTAGGGCCATACTCTGC 61.054 60.000 26.72 10.63 39.65 4.26
1848 1937 1.923395 CAGTTCCTGGGTAGGGCCA 60.923 63.158 6.18 0.00 44.70 5.36
2027 2116 7.416326 GCTTCTAGAAACTTGGACAAAGGAAAA 60.416 37.037 6.63 0.00 40.51 2.29
2039 2128 2.096218 GCACACCGCTTCTAGAAACTTG 60.096 50.000 6.63 4.96 37.77 3.16
2101 2190 1.963515 GAGTGGACAACAAAGCCCATT 59.036 47.619 0.00 0.00 0.00 3.16
2162 2252 8.131847 TGTGATCCAATTTTGAAACCATGATA 57.868 30.769 0.00 0.00 0.00 2.15
2345 2435 6.916387 CAGCAAATACATAAGAATCTTGGCAG 59.084 38.462 5.64 0.00 0.00 4.85
2371 2461 7.342194 CAGAAGATTTGTTTCAACTGCAATTG 58.658 34.615 0.36 0.36 0.00 2.32
2377 2467 5.973565 GTCACCAGAAGATTTGTTTCAACTG 59.026 40.000 0.00 0.00 0.00 3.16
2394 2484 8.515414 TCAATCGATATCTACATTAGTCACCAG 58.485 37.037 0.00 0.00 0.00 4.00
2396 2486 8.297426 TGTCAATCGATATCTACATTAGTCACC 58.703 37.037 0.00 0.00 0.00 4.02
2443 2533 7.234988 ACCTAAGCTAAGAACTAAAGAAGGTGA 59.765 37.037 0.00 0.00 31.48 4.02
2444 2534 7.387643 ACCTAAGCTAAGAACTAAAGAAGGTG 58.612 38.462 0.00 0.00 31.48 4.00
2445 2535 7.556416 ACCTAAGCTAAGAACTAAAGAAGGT 57.444 36.000 0.00 0.00 0.00 3.50
2515 2605 9.351570 CCTAAACTAAGAACTAAAGAAGGTACG 57.648 37.037 0.00 0.00 0.00 3.67
3012 3102 4.567971 AGCTCAGAAACAGACTCATCTTG 58.432 43.478 0.00 0.00 30.42 3.02
3126 3216 8.225603 ACAACTTCTATTCAAACACAAGATGT 57.774 30.769 0.00 0.00 46.42 3.06
3228 3318 8.041829 CAAATATGGATTCCAGATCTGATGAC 57.958 38.462 24.62 11.89 34.02 3.06
3343 3433 7.337942 AGAATGGTCGATTTGAAGCTAAGAATT 59.662 33.333 0.00 0.00 0.00 2.17
3368 3458 5.560966 AAAATGCATTCCGTGGTACTAAG 57.439 39.130 13.38 0.00 0.00 2.18
3428 3519 7.639945 CCGGAAAGGACTGATTAATATTTGAC 58.360 38.462 0.00 0.00 45.00 3.18
3470 3561 5.539955 TCGAATCATCTGGTGATCCTATCAA 59.460 40.000 3.48 0.00 46.80 2.57
3965 4056 4.686091 TCGTCTGATCACATTGTGTTCTTC 59.314 41.667 22.13 13.59 34.50 2.87
3971 4062 6.038985 AGATTAGTCGTCTGATCACATTGTG 58.961 40.000 14.83 10.64 38.59 3.33
3980 4071 7.174253 GTCCAAGATCTAGATTAGTCGTCTGAT 59.826 40.741 6.70 0.00 0.00 2.90
4001 4092 1.348064 ATGAACCTCCTCACGTCCAA 58.652 50.000 0.00 0.00 0.00 3.53
4006 4097 1.471676 GCCTGTATGAACCTCCTCACG 60.472 57.143 0.00 0.00 0.00 4.35
4007 4098 1.834263 AGCCTGTATGAACCTCCTCAC 59.166 52.381 0.00 0.00 0.00 3.51
4074 4167 2.035632 ACGGGGCACAATTTTCAAGAA 58.964 42.857 0.00 0.00 0.00 2.52
4190 4283 2.254546 ATCGGCACAGACAAGAAACA 57.745 45.000 0.00 0.00 0.00 2.83
4200 4293 0.670546 ACAACGGAGAATCGGCACAG 60.671 55.000 0.00 0.00 39.30 3.66
4207 4302 3.914312 TGAACTGAGACAACGGAGAATC 58.086 45.455 0.00 0.00 0.00 2.52
4214 4309 7.431960 TGAAATTCAAAATGAACTGAGACAACG 59.568 33.333 0.00 0.00 39.45 4.10
4383 4478 9.906660 CCCAATAAGCGAGCATAAAATAAATAA 57.093 29.630 0.00 0.00 0.00 1.40
4445 4540 1.620323 CTTCAGAAAGGCCCCAAAAGG 59.380 52.381 0.00 0.00 0.00 3.11
4505 4600 9.106070 AGAGTTTATTCAATCAACCGGTATAAC 57.894 33.333 8.00 0.00 0.00 1.89
4558 4654 9.174166 ACATGGGATGTTTAAATAAGTGTAGAC 57.826 33.333 0.00 0.00 41.63 2.59
4720 4820 2.477825 AGTGCGCAGAATAGCATGTAG 58.522 47.619 12.22 0.00 45.69 2.74
4734 4834 5.346522 ACTAATAACCAAGTACTAGTGCGC 58.653 41.667 5.39 0.00 0.00 6.09
4756 4856 9.326413 TGCTGTCTTTTAAGCTTAAGGATATAC 57.674 33.333 17.91 12.10 40.21 1.47
4774 4879 0.806868 CCATGCGTTCATGCTGTCTT 59.193 50.000 0.03 0.00 46.69 3.01
4776 4881 0.097674 GACCATGCGTTCATGCTGTC 59.902 55.000 0.03 0.67 46.69 3.51
4816 4921 2.676076 CTTTTGCCAAATTCCCGTGAG 58.324 47.619 0.00 0.00 0.00 3.51
4819 4924 3.605013 GCTTTTGCCAAATTCCCGT 57.395 47.368 0.00 0.00 40.15 5.28
4846 4951 0.321564 TGGACGGTGAATGGCTTGAG 60.322 55.000 0.00 0.00 0.00 3.02
4871 4976 3.958147 AATGTCGGCGGGCTCACTG 62.958 63.158 7.21 0.00 0.00 3.66
4872 4977 3.706373 AATGTCGGCGGGCTCACT 61.706 61.111 7.21 0.00 0.00 3.41
4873 4978 3.499737 CAATGTCGGCGGGCTCAC 61.500 66.667 7.21 0.00 0.00 3.51
4874 4979 3.545124 AACAATGTCGGCGGGCTCA 62.545 57.895 7.21 2.13 0.00 4.26
4875 4980 2.746277 AACAATGTCGGCGGGCTC 60.746 61.111 7.21 0.00 0.00 4.70
4876 4981 3.055719 CAACAATGTCGGCGGGCT 61.056 61.111 7.21 0.00 0.00 5.19
4877 4982 4.776647 GCAACAATGTCGGCGGGC 62.777 66.667 7.21 0.57 0.00 6.13
4878 4983 3.361158 TGCAACAATGTCGGCGGG 61.361 61.111 7.21 0.00 0.00 6.13
4879 4984 2.126888 GTGCAACAATGTCGGCGG 60.127 61.111 7.21 0.00 36.32 6.13


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

AutoCloner maintained by Alex Coulton.