Multiple sequence alignment - TraesCS5B01G357400

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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 TraesCS5B01G357400 chr5B 100.000 2822 0 0 1 2822 536655674 536658495 0.000000e+00 5212
1 TraesCS5B01G357400 chr5D 90.782 2853 122 47 1 2821 441098181 441100924 0.000000e+00 3681
2 TraesCS5B01G357400 chr5A 87.518 2059 87 69 789 2811 557314530 557316454 0.000000e+00 2222
3 TraesCS5B01G357400 chr5A 83.004 253 16 14 411 647 557313958 557314199 1.330000e-48 204
4 TraesCS5B01G357400 chr6B 77.363 455 82 12 1234 1673 717968691 717968243 1.680000e-62 250
5 TraesCS5B01G357400 chr6D 79.706 340 55 9 1234 1563 472897338 472897003 1.690000e-57 233
6 TraesCS5B01G357400 chr6A 79.042 334 59 7 1234 1563 616916961 616917287 4.730000e-53 219
7 TraesCS5B01G357400 chr4B 89.024 164 12 3 2030 2191 225958394 225958553 6.170000e-47 198
8 TraesCS5B01G357400 chr4B 88.415 164 13 3 2030 2191 199055598 199055757 2.870000e-45 193
9 TraesCS5B01G357400 chr7B 87.805 164 12 4 2030 2191 604278395 604278552 4.800000e-43 185
10 TraesCS5B01G357400 chr7A 88.125 160 13 3 2030 2187 474143105 474142950 4.800000e-43 185
11 TraesCS5B01G357400 chr2A 87.195 164 15 3 2030 2191 315960044 315960203 6.210000e-42 182


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 TraesCS5B01G357400 chr5B 536655674 536658495 2821 False 5212 5212 100.000 1 2822 1 chr5B.!!$F1 2821
1 TraesCS5B01G357400 chr5D 441098181 441100924 2743 False 3681 3681 90.782 1 2821 1 chr5D.!!$F1 2820
2 TraesCS5B01G357400 chr5A 557313958 557316454 2496 False 1213 2222 85.261 411 2811 2 chr5A.!!$F1 2400

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
333 335 0.107831 TCAAAGGACGGTTGGACCAG 59.892 55.0 0.0 0.0 38.47 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2409 0.173029 TGACGCCGATTAACCGCTAA 59.827 50.0 0.0 0.0 0.0 3.09 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 2.816689 ACCTTTTAAACGCTTGCCAAC 58.183 42.857 0.00 0.00 0.00 3.77
51 53 5.970592 TCTTGACGAGTCAGATGAATGATT 58.029 37.500 6.03 0.00 41.13 2.57
63 65 9.512435 GTCAGATGAATGATTTTATCAACCTTG 57.488 33.333 6.27 0.00 43.50 3.61
73 75 8.071368 TGATTTTATCAACCTTGACGTTTACAC 58.929 33.333 0.00 0.00 40.49 2.90
74 76 5.927954 TTATCAACCTTGACGTTTACACC 57.072 39.130 0.00 0.00 40.49 4.16
87 89 4.692155 ACGTTTACACCCAGTAGCAAATAC 59.308 41.667 0.00 0.00 33.43 1.89
99 101 6.583050 CCAGTAGCAAATACGCTAACTATCTC 59.417 42.308 0.00 0.00 45.72 2.75
142 144 5.516339 CCAACAAGCAGTTCACTTTACAAAG 59.484 40.000 0.13 0.13 38.74 2.77
151 153 4.447138 TCACTTTACAAAGGACCCATGT 57.553 40.909 6.66 5.22 40.31 3.21
174 176 2.629137 TGCAAGGGTAAGACGAACTACA 59.371 45.455 0.00 0.00 0.00 2.74
187 189 2.597305 CGAACTACATTCACACGCCTAC 59.403 50.000 0.00 0.00 37.12 3.18
196 198 5.472137 ACATTCACACGCCTACTTAATTTGT 59.528 36.000 0.00 0.00 0.00 2.83
200 202 6.923012 TCACACGCCTACTTAATTTGTACTA 58.077 36.000 0.00 0.00 0.00 1.82
233 235 0.841289 TCCCCGAGACAACAAACCTT 59.159 50.000 0.00 0.00 0.00 3.50
237 239 2.884639 CCCGAGACAACAAACCTTTGAT 59.115 45.455 4.77 0.00 40.55 2.57
260 262 0.534203 ATTCACCTGGTTCGCGTGTT 60.534 50.000 5.77 0.00 0.00 3.32
261 263 1.433053 TTCACCTGGTTCGCGTGTTG 61.433 55.000 5.77 0.00 0.00 3.33
262 264 3.276846 ACCTGGTTCGCGTGTTGC 61.277 61.111 5.77 0.00 41.47 4.17
275 277 3.155998 GCGTGTTGCGATATATCAATGC 58.844 45.455 13.11 8.54 44.77 3.56
276 278 3.736213 CGTGTTGCGATATATCAATGCC 58.264 45.455 13.11 0.00 44.77 4.40
277 279 3.186205 CGTGTTGCGATATATCAATGCCA 59.814 43.478 13.11 0.00 44.77 4.92
332 334 0.768622 ATCAAAGGACGGTTGGACCA 59.231 50.000 0.00 0.00 38.47 4.02
333 335 0.107831 TCAAAGGACGGTTGGACCAG 59.892 55.000 0.00 0.00 38.47 4.00
343 345 1.133915 GGTTGGACCAGTGAAGGAACA 60.134 52.381 0.00 0.00 38.42 3.18
360 362 3.375299 GGAACATAAGCATCACTGGTCAC 59.625 47.826 0.00 0.00 31.28 3.67
390 392 2.101582 ACAGTCTCACGAATAGCATCCC 59.898 50.000 0.00 0.00 0.00 3.85
394 396 2.705658 TCTCACGAATAGCATCCCCAAT 59.294 45.455 0.00 0.00 0.00 3.16
409 411 3.193267 TCCCCAATGAAGAATTTCGCAAG 59.807 43.478 0.34 0.00 36.04 4.01
430 432 5.695851 AGGTACAAGACAAAGATGCAAAG 57.304 39.130 0.00 0.00 0.00 2.77
495 505 3.124297 CCAAAGCAAAGCGAAAAACACAA 59.876 39.130 0.00 0.00 0.00 3.33
496 506 4.325386 CAAAGCAAAGCGAAAAACACAAG 58.675 39.130 0.00 0.00 0.00 3.16
658 679 2.972505 CCAAGACACGCAACCGCT 60.973 61.111 0.00 0.00 38.22 5.52
659 680 2.249309 CAAGACACGCAACCGCTG 59.751 61.111 0.00 0.00 38.22 5.18
736 757 0.251073 CGCCCCCTTTATATACCCCG 59.749 60.000 0.00 0.00 0.00 5.73
743 764 1.911357 CTTTATATACCCCGGGACCCC 59.089 57.143 26.32 0.00 0.00 4.95
745 766 1.178951 TATATACCCCGGGACCCCTT 58.821 55.000 26.32 4.40 0.00 3.95
747 768 2.330823 TATACCCCGGGACCCCTTCC 62.331 65.000 26.32 0.00 45.00 3.46
891 1105 0.730840 GGCGAACGGAATCGGATTTT 59.269 50.000 4.47 0.00 42.93 1.82
901 1115 0.180406 ATCGGATTTTGGGAGGGACG 59.820 55.000 0.00 0.00 0.00 4.79
902 1116 1.451387 CGGATTTTGGGAGGGACGG 60.451 63.158 0.00 0.00 0.00 4.79
963 1177 0.250901 AAGCAGCGAGTGATTTGGGT 60.251 50.000 0.00 0.00 27.05 4.51
1602 1837 4.176851 GGCGAGGACGACGAGGAC 62.177 72.222 0.00 0.00 42.66 3.85
1603 1838 4.517703 GCGAGGACGACGAGGACG 62.518 72.222 0.00 3.46 42.66 4.79
1604 1839 2.812609 CGAGGACGACGAGGACGA 60.813 66.667 0.00 0.00 41.06 4.20
1793 2037 4.717629 CAACAGCGACGAGGCGGA 62.718 66.667 0.00 0.00 38.18 5.54
1794 2038 4.719369 AACAGCGACGAGGCGGAC 62.719 66.667 0.00 0.00 38.18 4.79
1886 2130 3.194116 TGTACATAGTTCACCGTCCCTTC 59.806 47.826 0.00 0.00 0.00 3.46
1887 2131 1.553704 ACATAGTTCACCGTCCCTTCC 59.446 52.381 0.00 0.00 0.00 3.46
1888 2132 1.831736 CATAGTTCACCGTCCCTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
1899 2146 2.652113 CCCTTCCTCCTCCTCCCCT 61.652 68.421 0.00 0.00 0.00 4.79
1968 2215 1.141053 AGCATCAGCATCAGCATCAGA 59.859 47.619 0.00 0.00 45.49 3.27
1969 2216 1.947456 GCATCAGCATCAGCATCAGAA 59.053 47.619 0.00 0.00 45.49 3.02
1970 2217 2.031595 GCATCAGCATCAGCATCAGAAG 60.032 50.000 0.00 0.00 45.49 2.85
1971 2218 1.664873 TCAGCATCAGCATCAGAAGC 58.335 50.000 0.00 0.00 45.49 3.86
1972 2219 1.065709 TCAGCATCAGCATCAGAAGCA 60.066 47.619 0.00 0.00 45.49 3.91
1973 2220 1.332065 CAGCATCAGCATCAGAAGCAG 59.668 52.381 0.00 0.00 45.49 4.24
1991 2238 2.223665 GCAGCAGTTCAATTAGCATCCC 60.224 50.000 0.00 0.00 0.00 3.85
2001 2248 3.567478 ATTAGCATCCCAGAACCAGTC 57.433 47.619 0.00 0.00 0.00 3.51
2004 2251 1.211457 AGCATCCCAGAACCAGTCATC 59.789 52.381 0.00 0.00 0.00 2.92
2014 2261 3.513515 AGAACCAGTCATCACTCTTCCTC 59.486 47.826 0.00 0.00 0.00 3.71
2018 2265 2.836981 CAGTCATCACTCTTCCTCCCTT 59.163 50.000 0.00 0.00 0.00 3.95
2019 2266 3.103742 AGTCATCACTCTTCCTCCCTTC 58.896 50.000 0.00 0.00 0.00 3.46
2020 2267 2.169561 GTCATCACTCTTCCTCCCTTCC 59.830 54.545 0.00 0.00 0.00 3.46
2021 2268 1.488393 CATCACTCTTCCTCCCTTCCC 59.512 57.143 0.00 0.00 0.00 3.97
2043 2290 2.852449 TCCTTGAATCCCCATAGCAGTT 59.148 45.455 0.00 0.00 0.00 3.16
2074 2321 0.904649 TGTGTCATCAGGTAGCCAGG 59.095 55.000 0.00 0.00 0.00 4.45
2093 2345 2.092212 AGGTCCATTCCATGTCCATGTC 60.092 50.000 6.53 0.00 37.11 3.06
2094 2346 2.301346 GTCCATTCCATGTCCATGTCC 58.699 52.381 6.53 0.00 37.11 4.02
2126 2378 4.220602 GCATTAGGAGTCAACCAAACCAAT 59.779 41.667 0.00 0.00 0.00 3.16
2127 2379 5.622233 GCATTAGGAGTCAACCAAACCAATC 60.622 44.000 0.00 0.00 0.00 2.67
2157 2409 7.680350 GCAAGCAATGTGTTCATGTAGATGTAT 60.680 37.037 0.00 0.00 34.19 2.29
2229 2501 3.567397 GTTCCTCTAGATCCAGTGCCTA 58.433 50.000 0.00 0.00 0.00 3.93
2235 2507 3.706594 TCTAGATCCAGTGCCTACCAAAG 59.293 47.826 0.00 0.00 0.00 2.77
2254 2526 1.204941 AGTCGGCATACAACTCCAGTC 59.795 52.381 0.00 0.00 0.00 3.51
2266 2538 6.026947 ACAACTCCAGTCATTAGTCAGTAC 57.973 41.667 0.00 0.00 0.00 2.73
2270 2542 5.591067 ACTCCAGTCATTAGTCAGTACTAGC 59.409 44.000 0.00 0.00 39.36 3.42
2271 2543 5.506708 TCCAGTCATTAGTCAGTACTAGCA 58.493 41.667 0.00 0.00 39.36 3.49
2272 2544 5.590663 TCCAGTCATTAGTCAGTACTAGCAG 59.409 44.000 0.00 0.00 39.36 4.24
2298 2570 7.218228 AGCATTTGTTGTGATTCTGAACATA 57.782 32.000 0.00 0.00 30.00 2.29
2305 2577 6.862608 TGTTGTGATTCTGAACATATTGTTGC 59.137 34.615 0.00 0.00 41.28 4.17
2345 2617 0.735978 TCTGTACCATTCTGTGCGCG 60.736 55.000 0.00 0.00 0.00 6.86
2412 2684 4.241555 GCGGCGAGACCCATGGAT 62.242 66.667 15.22 0.00 33.26 3.41
2449 2721 5.837438 AGCCGTGGGAGTTTTATACTACTAT 59.163 40.000 0.00 0.00 37.87 2.12
2450 2722 7.006509 AGCCGTGGGAGTTTTATACTACTATA 58.993 38.462 0.00 0.00 37.87 1.31
2451 2723 7.040132 AGCCGTGGGAGTTTTATACTACTATAC 60.040 40.741 0.00 0.00 37.87 1.47
2505 2789 3.940640 CTGTGCTTGCGTGCGTGT 61.941 61.111 0.00 0.00 35.36 4.49
2506 2790 4.235025 TGTGCTTGCGTGCGTGTG 62.235 61.111 0.00 0.00 35.36 3.82
2507 2791 4.236416 GTGCTTGCGTGCGTGTGT 62.236 61.111 0.00 0.00 35.36 3.72
2508 2792 4.235025 TGCTTGCGTGCGTGTGTG 62.235 61.111 0.00 0.00 35.36 3.82
2560 2844 2.574399 GGACTCGCTCCTGTGGAC 59.426 66.667 0.00 0.00 35.89 4.02
2630 2915 1.542187 GCTTGGTAGGTCGGTCAGGT 61.542 60.000 0.00 0.00 0.00 4.00
2671 2962 1.538047 CCATTCTGAACTGGGTGGTG 58.462 55.000 9.60 0.00 0.00 4.17
2672 2963 1.538047 CATTCTGAACTGGGTGGTGG 58.462 55.000 0.00 0.00 0.00 4.61
2673 2964 1.149101 ATTCTGAACTGGGTGGTGGT 58.851 50.000 0.00 0.00 0.00 4.16
2674 2965 0.182537 TTCTGAACTGGGTGGTGGTG 59.817 55.000 0.00 0.00 0.00 4.17
2675 2966 0.692756 TCTGAACTGGGTGGTGGTGA 60.693 55.000 0.00 0.00 0.00 4.02
2676 2967 0.401738 CTGAACTGGGTGGTGGTGAT 59.598 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.802816 CTGACTCGTCAAGAAAGGGTTG 59.197 50.000 1.02 0.00 39.39 3.77
51 53 5.239087 GGGTGTAAACGTCAAGGTTGATAAA 59.761 40.000 0.00 0.00 39.73 1.40
63 65 2.443887 TGCTACTGGGTGTAAACGTC 57.556 50.000 0.00 0.00 0.00 4.34
73 75 3.793559 AGTTAGCGTATTTGCTACTGGG 58.206 45.455 0.00 0.00 46.57 4.45
74 76 6.448006 AGATAGTTAGCGTATTTGCTACTGG 58.552 40.000 0.00 0.00 46.57 4.00
99 101 2.168521 TGGCTTCGAAACTCTCCTATGG 59.831 50.000 0.00 0.00 0.00 2.74
142 144 3.685435 CCTTGCACACATGGGTCC 58.315 61.111 0.00 0.00 37.44 4.46
151 153 1.414919 AGTTCGTCTTACCCTTGCACA 59.585 47.619 0.00 0.00 0.00 4.57
174 176 6.877322 AGTACAAATTAAGTAGGCGTGTGAAT 59.123 34.615 0.00 0.00 0.00 2.57
196 198 4.100498 CGGGGAAGGAACATTAGCTTAGTA 59.900 45.833 0.00 0.00 0.00 1.82
200 202 1.913419 TCGGGGAAGGAACATTAGCTT 59.087 47.619 0.00 0.00 0.00 3.74
215 217 1.336755 CAAAGGTTTGTTGTCTCGGGG 59.663 52.381 0.00 0.00 33.59 5.73
233 235 3.599343 CGAACCAGGTGAATGAGATCAA 58.401 45.455 0.00 0.00 0.00 2.57
237 239 0.389817 CGCGAACCAGGTGAATGAGA 60.390 55.000 0.00 0.00 0.00 3.27
260 262 3.127376 GCACATGGCATTGATATATCGCA 59.873 43.478 8.19 0.00 43.97 5.10
261 263 3.688272 GCACATGGCATTGATATATCGC 58.312 45.455 8.19 5.52 43.97 4.58
311 313 1.271163 GGTCCAACCGTCCTTTGATGA 60.271 52.381 0.00 0.00 0.00 2.92
332 334 4.940046 CAGTGATGCTTATGTTCCTTCACT 59.060 41.667 0.00 0.00 41.66 3.41
333 335 4.095483 CCAGTGATGCTTATGTTCCTTCAC 59.905 45.833 0.00 0.00 35.25 3.18
343 345 1.743772 GCGGTGACCAGTGATGCTTAT 60.744 52.381 1.11 0.00 0.00 1.73
360 362 3.416119 TCGTGAGACTGTATTTAGCGG 57.584 47.619 0.00 0.00 33.31 5.52
390 392 4.178545 ACCTTGCGAAATTCTTCATTGG 57.821 40.909 0.00 0.00 0.00 3.16
394 396 5.049680 GTCTTGTACCTTGCGAAATTCTTCA 60.050 40.000 0.00 0.00 0.00 3.02
409 411 4.229876 GCTTTGCATCTTTGTCTTGTACC 58.770 43.478 0.00 0.00 0.00 3.34
471 481 1.003972 GTTTTTCGCTTTGCTTTGGGC 60.004 47.619 0.00 0.00 42.22 5.36
510 527 3.424433 CGGTTTGGTTCTTCATCGCTTAC 60.424 47.826 0.00 0.00 0.00 2.34
634 655 2.028484 GCGTGTCTTGGACGGACA 59.972 61.111 0.00 0.00 40.78 4.02
714 735 0.034767 GGTATATAAAGGGGGCGGGC 60.035 60.000 0.00 0.00 0.00 6.13
715 736 0.622136 GGGTATATAAAGGGGGCGGG 59.378 60.000 0.00 0.00 0.00 6.13
717 738 0.251073 CGGGGTATATAAAGGGGGCG 59.749 60.000 0.00 0.00 0.00 6.13
718 739 0.622136 CCGGGGTATATAAAGGGGGC 59.378 60.000 0.00 0.00 0.00 5.80
721 742 1.911357 GGTCCCGGGGTATATAAAGGG 59.089 57.143 23.50 6.70 40.16 3.95
743 764 4.120755 GGCAGGGCAGAGGGGAAG 62.121 72.222 0.00 0.00 0.00 3.46
745 766 3.694697 TAGGCAGGGCAGAGGGGA 61.695 66.667 0.00 0.00 0.00 4.81
747 768 3.854669 CGTAGGCAGGGCAGAGGG 61.855 72.222 0.00 0.00 0.00 4.30
901 1115 2.124278 GGGATCCAAACGCCTCCC 60.124 66.667 15.23 0.00 40.60 4.30
902 1116 0.395724 AATGGGATCCAAACGCCTCC 60.396 55.000 15.23 0.00 36.95 4.30
950 1164 1.449601 CCCCGACCCAAATCACTCG 60.450 63.158 0.00 0.00 0.00 4.18
952 1166 1.280998 CTAACCCCGACCCAAATCACT 59.719 52.381 0.00 0.00 0.00 3.41
963 1177 0.618393 ATCCGAAACCCTAACCCCGA 60.618 55.000 0.00 0.00 0.00 5.14
1035 1270 4.673298 CACACCTGGTACGGCGCA 62.673 66.667 10.83 0.00 0.00 6.09
1410 1645 1.754745 GCGGATGAGGCCCTTCATA 59.245 57.895 7.44 0.00 37.90 2.15
1774 2018 4.717629 CGCCTCGTCGCTGTTGGA 62.718 66.667 0.00 0.00 0.00 3.53
1886 2130 1.382420 CACAGAGGGGAGGAGGAGG 60.382 68.421 0.00 0.00 0.00 4.30
1887 2131 2.063378 GCACAGAGGGGAGGAGGAG 61.063 68.421 0.00 0.00 0.00 3.69
1888 2132 2.039624 GCACAGAGGGGAGGAGGA 59.960 66.667 0.00 0.00 0.00 3.71
1899 2146 0.829990 TCTGTTGACACCTGCACAGA 59.170 50.000 3.32 3.32 32.63 3.41
1968 2215 3.129988 GGATGCTAATTGAACTGCTGCTT 59.870 43.478 0.00 0.00 0.00 3.91
1969 2216 2.686915 GGATGCTAATTGAACTGCTGCT 59.313 45.455 0.00 0.00 0.00 4.24
1970 2217 2.223665 GGGATGCTAATTGAACTGCTGC 60.224 50.000 0.00 0.00 0.00 5.25
1971 2218 3.018856 TGGGATGCTAATTGAACTGCTG 58.981 45.455 0.00 0.00 0.00 4.41
1972 2219 3.054139 TCTGGGATGCTAATTGAACTGCT 60.054 43.478 0.00 0.00 0.00 4.24
1973 2220 3.282021 TCTGGGATGCTAATTGAACTGC 58.718 45.455 0.00 0.00 0.00 4.40
1991 2238 3.260380 AGGAAGAGTGATGACTGGTTCTG 59.740 47.826 0.00 0.00 30.16 3.02
2001 2248 1.488393 GGGAAGGGAGGAAGAGTGATG 59.512 57.143 0.00 0.00 0.00 3.07
2004 2251 1.199615 GAGGGAAGGGAGGAAGAGTG 58.800 60.000 0.00 0.00 0.00 3.51
2014 2261 0.553333 GGGATTCAAGGAGGGAAGGG 59.447 60.000 0.00 0.00 0.00 3.95
2018 2265 2.706350 CTATGGGGATTCAAGGAGGGA 58.294 52.381 0.00 0.00 0.00 4.20
2019 2266 1.074566 GCTATGGGGATTCAAGGAGGG 59.925 57.143 0.00 0.00 0.00 4.30
2020 2267 1.776667 TGCTATGGGGATTCAAGGAGG 59.223 52.381 0.00 0.00 0.00 4.30
2021 2268 2.441001 ACTGCTATGGGGATTCAAGGAG 59.559 50.000 0.00 0.00 0.00 3.69
2043 2290 4.142381 CCTGATGACACAACTACAGATCGA 60.142 45.833 0.00 0.00 0.00 3.59
2093 2345 1.683917 ACTCCTAATGCTGCTACGAGG 59.316 52.381 0.00 2.79 0.00 4.63
2094 2346 2.359214 TGACTCCTAATGCTGCTACGAG 59.641 50.000 0.00 1.62 0.00 4.18
2126 2378 2.030371 TGAACACATTGCTTGCTTGGA 58.970 42.857 0.00 0.00 0.00 3.53
2127 2379 2.512485 TGAACACATTGCTTGCTTGG 57.488 45.000 0.00 0.00 0.00 3.61
2157 2409 0.173029 TGACGCCGATTAACCGCTAA 59.827 50.000 0.00 0.00 0.00 3.09
2229 2501 2.423577 GAGTTGTATGCCGACTTTGGT 58.576 47.619 0.00 0.00 37.96 3.67
2235 2507 1.067142 TGACTGGAGTTGTATGCCGAC 60.067 52.381 0.00 0.00 0.00 4.79
2242 2514 6.946583 AGTACTGACTAATGACTGGAGTTGTA 59.053 38.462 0.00 0.00 32.65 2.41
2254 2526 6.378710 TGCTACTGCTAGTACTGACTAATG 57.621 41.667 5.39 0.00 37.72 1.90
2266 2538 5.808042 ATCACAACAAATGCTACTGCTAG 57.192 39.130 0.00 0.00 40.48 3.42
2270 2542 6.245115 TCAGAATCACAACAAATGCTACTG 57.755 37.500 0.00 0.00 0.00 2.74
2271 2543 6.262944 TGTTCAGAATCACAACAAATGCTACT 59.737 34.615 0.00 0.00 0.00 2.57
2272 2544 6.437928 TGTTCAGAATCACAACAAATGCTAC 58.562 36.000 0.00 0.00 0.00 3.58
2298 2570 6.046593 CAGAATGCAATAATGGAGCAACAAT 58.953 36.000 0.00 0.00 42.15 2.71
2345 2617 0.107312 AGCATCTGGTGAGCATGGAC 60.107 55.000 0.00 0.00 0.00 4.02
2412 2684 2.369633 ACGGCTGCTGGATCCATCA 61.370 57.895 16.63 16.91 0.00 3.07
2503 2787 2.101185 CAAAACCGCACGCACACA 59.899 55.556 0.00 0.00 0.00 3.72
2504 2788 2.653766 CCAAAACCGCACGCACAC 60.654 61.111 0.00 0.00 0.00 3.82
2505 2789 4.560856 GCCAAAACCGCACGCACA 62.561 61.111 0.00 0.00 0.00 4.57
2509 2793 3.342627 TCTCGCCAAAACCGCACG 61.343 61.111 0.00 0.00 0.00 5.34
2510 2794 2.251371 GTCTCGCCAAAACCGCAC 59.749 61.111 0.00 0.00 0.00 5.34
2511 2795 3.342627 CGTCTCGCCAAAACCGCA 61.343 61.111 0.00 0.00 0.00 5.69
2512 2796 3.343421 ACGTCTCGCCAAAACCGC 61.343 61.111 0.00 0.00 0.00 5.68
2513 2797 2.549282 CACGTCTCGCCAAAACCG 59.451 61.111 0.00 0.00 0.00 4.44
2514 2798 2.943653 CCACGTCTCGCCAAAACC 59.056 61.111 0.00 0.00 0.00 3.27
2515 2799 2.251371 GCCACGTCTCGCCAAAAC 59.749 61.111 0.00 0.00 0.00 2.43
2581 2865 4.922026 AACGCACCGTCCACCACC 62.922 66.667 0.00 0.00 39.99 4.61
2582 2866 3.645975 CAACGCACCGTCCACCAC 61.646 66.667 0.00 0.00 39.99 4.16
2583 2867 3.800685 CTCAACGCACCGTCCACCA 62.801 63.158 0.00 0.00 39.99 4.17
2584 2868 3.041940 CTCAACGCACCGTCCACC 61.042 66.667 0.00 0.00 39.99 4.61
2585 2869 2.279918 ACTCAACGCACCGTCCAC 60.280 61.111 0.00 0.00 39.99 4.02
2586 2870 2.279851 CACTCAACGCACCGTCCA 60.280 61.111 0.00 0.00 39.99 4.02
2587 2871 3.712881 GCACTCAACGCACCGTCC 61.713 66.667 0.00 0.00 39.99 4.79
2608 2893 4.078516 ACCGACCTACCAAGCCGC 62.079 66.667 0.00 0.00 0.00 6.53
2614 2899 0.611062 CTGACCTGACCGACCTACCA 60.611 60.000 0.00 0.00 0.00 3.25
2658 2943 0.110295 CATCACCACCACCCAGTTCA 59.890 55.000 0.00 0.00 0.00 3.18
2671 2962 2.035626 CCCACCACCACCATCACC 59.964 66.667 0.00 0.00 0.00 4.02
2672 2963 2.035626 CCCCACCACCACCATCAC 59.964 66.667 0.00 0.00 0.00 3.06
2673 2964 3.978193 GCCCCACCACCACCATCA 61.978 66.667 0.00 0.00 0.00 3.07
2749 3044 0.456653 GTCACATCGCCATTGCCAAC 60.457 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.