Multiple sequence alignment - TraesCS2D01G472000

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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 TraesCS2D01G472000 chr2D 100.000 2784 0 0 1 2784 575771610 575768827 0.000000e+00 5142.0
1 TraesCS2D01G472000 chr2D 89.642 531 50 3 2256 2784 531768810 531769337 0.000000e+00 671.0
2 TraesCS2D01G472000 chr2B 91.643 2788 134 37 47 2784 691811743 691809005 0.000000e+00 3766.0
3 TraesCS2D01G472000 chr2B 86.177 586 68 8 2205 2784 631607678 631608256 3.050000e-174 621.0
4 TraesCS2D01G472000 chr2A 89.429 2138 116 40 91 2186 713937276 713935207 0.000000e+00 2595.0
5 TraesCS2D01G472000 chr4A 88.488 582 57 6 2205 2784 736822603 736822030 0.000000e+00 695.0
6 TraesCS2D01G472000 chr4A 87.136 583 64 6 2205 2784 735742131 735741557 0.000000e+00 651.0
7 TraesCS2D01G472000 chr4A 87.166 561 66 6 2222 2778 17781470 17780912 1.410000e-177 632.0
8 TraesCS2D01G472000 chr6B 88.133 573 62 5 2204 2772 688752578 688753148 0.000000e+00 676.0
9 TraesCS2D01G472000 chr1D 87.108 574 66 6 2206 2778 475867904 475867338 0.000000e+00 643.0
10 TraesCS2D01G472000 chr1B 87.321 560 63 8 2211 2770 661931966 661931415 3.910000e-178 634.0
11 TraesCS2D01G472000 chr5B 88.356 146 14 2 1464 1609 423225695 423225837 3.690000e-39 172.0
12 TraesCS2D01G472000 chr5B 82.993 147 22 3 1253 1399 423225523 423225666 2.250000e-26 130.0
13 TraesCS2D01G472000 chr5B 89.011 91 10 0 1050 1140 423225352 423225442 2.270000e-21 113.0
14 TraesCS2D01G472000 chr5D 91.304 92 8 0 1050 1141 358010362 358010453 2.910000e-25 126.0
15 TraesCS2D01G472000 chr5A 90.110 91 9 0 1050 1140 458966879 458966969 4.870000e-23 119.0
16 TraesCS2D01G472000 chr5A 81.879 149 20 6 1253 1399 458967050 458967193 4.870000e-23 119.0
17 TraesCS2D01G472000 chr3A 100.000 28 0 0 2206 2233 724558333 724558360 5.000000e-03 52.8


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 TraesCS2D01G472000 chr2D 575768827 575771610 2783 True 5142 5142 100.000 1 2784 1 chr2D.!!$R1 2783
1 TraesCS2D01G472000 chr2D 531768810 531769337 527 False 671 671 89.642 2256 2784 1 chr2D.!!$F1 528
2 TraesCS2D01G472000 chr2B 691809005 691811743 2738 True 3766 3766 91.643 47 2784 1 chr2B.!!$R1 2737
3 TraesCS2D01G472000 chr2B 631607678 631608256 578 False 621 621 86.177 2205 2784 1 chr2B.!!$F1 579
4 TraesCS2D01G472000 chr2A 713935207 713937276 2069 True 2595 2595 89.429 91 2186 1 chr2A.!!$R1 2095
5 TraesCS2D01G472000 chr4A 736822030 736822603 573 True 695 695 88.488 2205 2784 1 chr4A.!!$R3 579
6 TraesCS2D01G472000 chr4A 735741557 735742131 574 True 651 651 87.136 2205 2784 1 chr4A.!!$R2 579
7 TraesCS2D01G472000 chr4A 17780912 17781470 558 True 632 632 87.166 2222 2778 1 chr4A.!!$R1 556
8 TraesCS2D01G472000 chr6B 688752578 688753148 570 False 676 676 88.133 2204 2772 1 chr6B.!!$F1 568
9 TraesCS2D01G472000 chr1D 475867338 475867904 566 True 643 643 87.108 2206 2778 1 chr1D.!!$R1 572
10 TraesCS2D01G472000 chr1B 661931415 661931966 551 True 634 634 87.321 2211 2770 1 chr1B.!!$R1 559

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
221 226 0.108615 CCTCGTCTTGCTTCATCGGT 60.109 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2171 0.106769 TGGGCAGAAGAACACAGCAA 60.107 50.0 0.0 0.0 0.0 3.91 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 4.898607 AGCAACACGTCAATGGGT 57.101 50.000 0.00 0.00 0.00 4.51
18 19 2.330254 AGCAACACGTCAATGGGTG 58.670 52.632 4.31 4.31 39.98 4.61
19 20 1.371635 GCAACACGTCAATGGGTGC 60.372 57.895 0.00 0.00 37.68 5.01
20 21 1.082169 CAACACGTCAATGGGTGCG 60.082 57.895 5.51 0.00 37.68 5.34
21 22 1.227704 AACACGTCAATGGGTGCGA 60.228 52.632 5.51 0.00 37.68 5.10
22 23 0.816018 AACACGTCAATGGGTGCGAA 60.816 50.000 5.51 0.00 37.68 4.70
23 24 1.206578 CACGTCAATGGGTGCGAAC 59.793 57.895 0.00 0.00 33.02 3.95
24 25 2.314647 ACGTCAATGGGTGCGAACG 61.315 57.895 0.00 0.00 32.71 3.95
25 26 2.867472 GTCAATGGGTGCGAACGG 59.133 61.111 0.00 0.00 0.00 4.44
26 27 2.359354 TCAATGGGTGCGAACGGG 60.359 61.111 0.00 0.00 0.00 5.28
27 28 2.359354 CAATGGGTGCGAACGGGA 60.359 61.111 0.00 0.00 0.00 5.14
28 29 2.046314 AATGGGTGCGAACGGGAG 60.046 61.111 0.00 0.00 0.00 4.30
29 30 3.622060 AATGGGTGCGAACGGGAGG 62.622 63.158 0.00 0.00 0.00 4.30
33 34 3.766691 GTGCGAACGGGAGGCCTA 61.767 66.667 4.42 0.00 0.00 3.93
34 35 3.458163 TGCGAACGGGAGGCCTAG 61.458 66.667 4.42 2.40 0.00 3.02
35 36 4.222847 GCGAACGGGAGGCCTAGG 62.223 72.222 4.42 3.67 0.00 3.02
36 37 4.222847 CGAACGGGAGGCCTAGGC 62.223 72.222 26.55 26.55 41.06 3.93
37 38 3.081409 GAACGGGAGGCCTAGGCA 61.081 66.667 34.09 0.00 44.11 4.75
38 39 2.609610 AACGGGAGGCCTAGGCAA 60.610 61.111 34.09 0.00 44.11 4.52
39 40 2.595009 GAACGGGAGGCCTAGGCAAG 62.595 65.000 34.09 20.82 44.11 4.01
40 41 4.554036 CGGGAGGCCTAGGCAAGC 62.554 72.222 34.09 21.40 44.11 4.01
41 42 3.411517 GGGAGGCCTAGGCAAGCA 61.412 66.667 34.09 0.00 44.11 3.91
42 43 2.761465 GGGAGGCCTAGGCAAGCAT 61.761 63.158 34.09 14.60 44.11 3.79
43 44 1.228510 GGAGGCCTAGGCAAGCATT 59.771 57.895 34.09 12.39 44.11 3.56
59 60 6.051646 CAAGCATTGGAAAAACAAAAGGAG 57.948 37.500 0.00 0.00 43.94 3.69
60 61 5.612725 AGCATTGGAAAAACAAAAGGAGA 57.387 34.783 0.00 0.00 33.48 3.71
73 74 1.719063 AAGGAGAGGTGCCTTTGCCA 61.719 55.000 0.00 0.00 42.99 4.92
78 79 2.029518 GGTGCCTTTGCCAAGCAC 59.970 61.111 12.05 12.05 38.71 4.40
79 80 2.795110 GGTGCCTTTGCCAAGCACA 61.795 57.895 19.49 7.19 38.71 4.57
80 81 1.300388 GTGCCTTTGCCAAGCACAG 60.300 57.895 14.74 3.40 38.71 3.66
88 89 4.034258 CCAAGCACAGGCAGCGTG 62.034 66.667 13.64 13.64 44.61 5.34
107 108 1.523711 CCGAATGACATGTCCCGGG 60.524 63.158 28.80 16.85 34.64 5.73
197 198 4.451150 GCACAGATCCCGGCGACA 62.451 66.667 9.30 0.00 0.00 4.35
212 217 1.078759 CGACATGTCCCTCGTCTTGC 61.079 60.000 20.03 0.00 0.00 4.01
218 223 1.066858 TGTCCCTCGTCTTGCTTCATC 60.067 52.381 0.00 0.00 0.00 2.92
219 224 0.173481 TCCCTCGTCTTGCTTCATCG 59.827 55.000 0.00 0.00 0.00 3.84
220 225 0.807667 CCCTCGTCTTGCTTCATCGG 60.808 60.000 0.00 0.00 0.00 4.18
221 226 0.108615 CCTCGTCTTGCTTCATCGGT 60.109 55.000 0.00 0.00 0.00 4.69
222 227 0.994995 CTCGTCTTGCTTCATCGGTG 59.005 55.000 0.00 0.00 0.00 4.94
320 325 3.138304 TCGAGGAATTTTGACCACTGTG 58.862 45.455 0.00 0.00 0.00 3.66
351 356 2.480555 CGCGCCCTTTTAGCAGTG 59.519 61.111 0.00 0.00 0.00 3.66
379 384 2.307049 GTTCAACATCGACAAAAGCCG 58.693 47.619 0.00 0.00 0.00 5.52
485 490 0.677414 TGATTCGCTTGCTGCCATGA 60.677 50.000 0.00 0.00 38.78 3.07
569 574 1.692148 TAATGAAGTTGGCGAGCGCG 61.692 55.000 5.14 5.14 43.06 6.86
593 598 3.628280 GACGCTCCGAAGCCGAGTT 62.628 63.158 0.00 0.00 46.34 3.01
909 918 0.804255 TCCTCCCTCTTAAACCCCCT 59.196 55.000 0.00 0.00 0.00 4.79
910 919 1.214217 CCTCCCTCTTAAACCCCCTC 58.786 60.000 0.00 0.00 0.00 4.30
911 920 1.274475 CCTCCCTCTTAAACCCCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
912 921 2.120312 CTCCCTCTTAAACCCCCTCTC 58.880 57.143 0.00 0.00 0.00 3.20
966 995 1.444119 GCTTCCACACAACGCTTCCA 61.444 55.000 0.00 0.00 0.00 3.53
976 1005 0.739813 AACGCTTCCACTGCCGATAC 60.740 55.000 0.00 0.00 0.00 2.24
977 1006 1.141881 CGCTTCCACTGCCGATACT 59.858 57.895 0.00 0.00 0.00 2.12
978 1007 0.384309 CGCTTCCACTGCCGATACTA 59.616 55.000 0.00 0.00 0.00 1.82
982 1011 1.019673 TCCACTGCCGATACTACGAC 58.980 55.000 0.00 0.00 35.09 4.34
983 1012 1.022735 CCACTGCCGATACTACGACT 58.977 55.000 0.00 0.00 35.09 4.18
994 1030 1.888215 ACTACGACTCCACGAGTGAA 58.112 50.000 4.59 0.00 43.53 3.18
1179 1221 3.845259 CCATGGGCATGCACCAGC 61.845 66.667 25.54 7.98 42.15 4.85
1195 1237 4.658063 CACCAGCCTAGTAGTAGCTCTAT 58.342 47.826 0.00 0.00 0.00 1.98
1199 1241 5.770663 CCAGCCTAGTAGTAGCTCTATTTCA 59.229 44.000 0.00 0.00 0.00 2.69
1201 1243 7.142680 CAGCCTAGTAGTAGCTCTATTTCAAC 58.857 42.308 0.00 0.00 0.00 3.18
1202 1244 6.265876 AGCCTAGTAGTAGCTCTATTTCAACC 59.734 42.308 0.00 0.00 0.00 3.77
1204 1246 5.517322 AGTAGTAGCTCTATTTCAACCGG 57.483 43.478 0.00 0.00 0.00 5.28
1205 1247 3.180891 AGTAGCTCTATTTCAACCGGC 57.819 47.619 0.00 0.00 0.00 6.13
1206 1248 2.500098 AGTAGCTCTATTTCAACCGGCA 59.500 45.455 0.00 0.00 0.00 5.69
1207 1249 2.717639 AGCTCTATTTCAACCGGCAT 57.282 45.000 0.00 0.00 0.00 4.40
1208 1250 3.004752 AGCTCTATTTCAACCGGCATT 57.995 42.857 0.00 0.00 0.00 3.56
1209 1251 2.684881 AGCTCTATTTCAACCGGCATTG 59.315 45.455 0.00 0.00 0.00 2.82
1210 1252 2.796032 GCTCTATTTCAACCGGCATTGC 60.796 50.000 0.00 0.00 0.00 3.56
1211 1253 1.748493 TCTATTTCAACCGGCATTGCC 59.252 47.619 18.10 18.10 46.75 4.52
1260 1307 3.887335 ATGGTTGGCCGCGTACGTT 62.887 57.895 17.90 0.00 37.70 3.99
1415 1462 1.079750 GACGACTGCCTCCTCAACC 60.080 63.158 0.00 0.00 0.00 3.77
1423 1470 4.452733 CTCCTCAACCGCGGACCC 62.453 72.222 35.90 0.00 0.00 4.46
1518 1565 2.512515 GCTCATGTCCGACCTGGC 60.513 66.667 4.23 3.55 37.80 4.85
1613 1660 2.204034 TCCTGGAGCTGGACCACA 59.796 61.111 0.00 0.00 33.57 4.17
1636 1683 4.680237 CACGAAGCCGGACCAGCA 62.680 66.667 5.05 0.00 40.78 4.41
1638 1685 3.121030 CGAAGCCGGACCAGCAAG 61.121 66.667 5.05 0.00 0.00 4.01
1640 1687 4.269523 AAGCCGGACCAGCAAGCA 62.270 61.111 5.05 0.00 0.00 3.91
1838 1897 1.353022 AGCAAAACGGAGGGGACAATA 59.647 47.619 0.00 0.00 0.00 1.90
1840 1899 1.735571 CAAAACGGAGGGGACAATACG 59.264 52.381 0.00 0.00 0.00 3.06
1845 1904 0.107848 GGAGGGGACAATACGGTGTG 60.108 60.000 0.00 0.00 0.00 3.82
1881 1945 0.814457 TTGCCTGTTTCGTGTTGCTT 59.186 45.000 0.00 0.00 0.00 3.91
1902 1977 1.153509 GGCCAACCTGCGTACGTAT 60.154 57.895 17.90 0.00 0.00 3.06
2011 2086 2.974698 GCAGCTTGGCTCGTGTGT 60.975 61.111 0.00 0.00 36.40 3.72
2090 2171 1.544724 ACAGTTGTGGTGCACTGTTT 58.455 45.000 17.98 0.00 36.66 2.83
2101 2185 1.818060 TGCACTGTTTTGCTGTGTTCT 59.182 42.857 6.22 0.00 45.27 3.01
2102 2186 2.230992 TGCACTGTTTTGCTGTGTTCTT 59.769 40.909 6.22 0.00 45.27 2.52
2103 2187 2.854185 GCACTGTTTTGCTGTGTTCTTC 59.146 45.455 6.22 0.00 45.27 2.87
2196 2282 4.023021 TGTTTTGTCTTAATAACACGGCCC 60.023 41.667 0.00 0.00 0.00 5.80
2233 2319 1.231221 AAAGACCGTGCGTTGCAATA 58.769 45.000 0.59 0.00 41.47 1.90
2343 2431 2.307098 CCTCCTTCCCACTCTTGTCAAT 59.693 50.000 0.00 0.00 0.00 2.57
2354 2442 0.109597 CTTGTCAATGGCGGCTTCAC 60.110 55.000 11.43 5.31 0.00 3.18
2373 2461 2.874086 CACTGCTCACAATCACAACTCA 59.126 45.455 0.00 0.00 0.00 3.41
2435 2524 8.370940 TCTCCGCATAAGATGAGAAATCTATTT 58.629 33.333 0.00 0.00 31.26 1.40
2462 2551 1.378119 CCTGGAGGTTTTACCGGGC 60.378 63.158 6.32 0.00 44.90 6.13
2486 2575 1.806542 GCATGCGTGGTTATAGATGGG 59.193 52.381 8.27 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.371635 GCACCCATTGACGTGTTGC 60.372 57.895 0.00 0.00 32.40 4.17
2 3 1.082169 CGCACCCATTGACGTGTTG 60.082 57.895 0.00 0.00 32.40 3.33
5 6 1.206578 GTTCGCACCCATTGACGTG 59.793 57.895 0.00 0.87 0.00 4.49
7 8 2.474266 CGTTCGCACCCATTGACG 59.526 61.111 0.00 0.00 0.00 4.35
8 9 2.686816 CCCGTTCGCACCCATTGAC 61.687 63.158 0.00 0.00 0.00 3.18
9 10 2.359354 CCCGTTCGCACCCATTGA 60.359 61.111 0.00 0.00 0.00 2.57
10 11 2.359354 TCCCGTTCGCACCCATTG 60.359 61.111 0.00 0.00 0.00 2.82
12 13 4.096003 CCTCCCGTTCGCACCCAT 62.096 66.667 0.00 0.00 0.00 4.00
16 17 3.718210 CTAGGCCTCCCGTTCGCAC 62.718 68.421 9.68 0.00 35.76 5.34
17 18 3.458163 CTAGGCCTCCCGTTCGCA 61.458 66.667 9.68 0.00 35.76 5.10
18 19 4.222847 CCTAGGCCTCCCGTTCGC 62.223 72.222 9.68 0.00 35.76 4.70
19 20 4.222847 GCCTAGGCCTCCCGTTCG 62.223 72.222 24.19 0.00 35.76 3.95
20 21 2.595009 CTTGCCTAGGCCTCCCGTTC 62.595 65.000 30.81 0.44 41.09 3.95
21 22 2.609610 TTGCCTAGGCCTCCCGTT 60.610 61.111 30.81 0.00 41.09 4.44
22 23 3.083997 CTTGCCTAGGCCTCCCGT 61.084 66.667 30.81 0.00 41.09 5.28
23 24 4.554036 GCTTGCCTAGGCCTCCCG 62.554 72.222 30.81 14.71 41.09 5.14
24 25 2.290021 AATGCTTGCCTAGGCCTCCC 62.290 60.000 30.81 16.25 41.09 4.30
25 26 1.105759 CAATGCTTGCCTAGGCCTCC 61.106 60.000 30.81 18.01 41.09 4.30
26 27 1.105759 CCAATGCTTGCCTAGGCCTC 61.106 60.000 30.81 18.93 41.09 4.70
27 28 1.076485 CCAATGCTTGCCTAGGCCT 60.076 57.895 30.81 11.78 41.09 5.19
28 29 0.684153 TTCCAATGCTTGCCTAGGCC 60.684 55.000 30.81 16.10 41.09 5.19
29 30 1.185315 TTTCCAATGCTTGCCTAGGC 58.815 50.000 27.71 27.71 42.35 3.93
30 31 3.006752 TGTTTTTCCAATGCTTGCCTAGG 59.993 43.478 3.67 3.67 0.00 3.02
31 32 4.255833 TGTTTTTCCAATGCTTGCCTAG 57.744 40.909 0.00 0.00 0.00 3.02
32 33 4.679373 TTGTTTTTCCAATGCTTGCCTA 57.321 36.364 0.00 0.00 0.00 3.93
33 34 3.557228 TTGTTTTTCCAATGCTTGCCT 57.443 38.095 0.00 0.00 0.00 4.75
34 35 4.497842 CCTTTTGTTTTTCCAATGCTTGCC 60.498 41.667 0.00 0.00 0.00 4.52
35 36 4.335037 TCCTTTTGTTTTTCCAATGCTTGC 59.665 37.500 0.00 0.00 0.00 4.01
36 37 5.816777 TCTCCTTTTGTTTTTCCAATGCTTG 59.183 36.000 0.00 0.00 0.00 4.01
37 38 5.988287 TCTCCTTTTGTTTTTCCAATGCTT 58.012 33.333 0.00 0.00 0.00 3.91
38 39 5.453762 CCTCTCCTTTTGTTTTTCCAATGCT 60.454 40.000 0.00 0.00 0.00 3.79
39 40 4.751600 CCTCTCCTTTTGTTTTTCCAATGC 59.248 41.667 0.00 0.00 0.00 3.56
40 41 5.754890 CACCTCTCCTTTTGTTTTTCCAATG 59.245 40.000 0.00 0.00 0.00 2.82
41 42 5.684813 GCACCTCTCCTTTTGTTTTTCCAAT 60.685 40.000 0.00 0.00 0.00 3.16
42 43 4.382577 GCACCTCTCCTTTTGTTTTTCCAA 60.383 41.667 0.00 0.00 0.00 3.53
43 44 3.132111 GCACCTCTCCTTTTGTTTTTCCA 59.868 43.478 0.00 0.00 0.00 3.53
44 45 3.492656 GGCACCTCTCCTTTTGTTTTTCC 60.493 47.826 0.00 0.00 0.00 3.13
45 46 3.384789 AGGCACCTCTCCTTTTGTTTTTC 59.615 43.478 0.00 0.00 0.00 2.29
46 47 3.374764 AGGCACCTCTCCTTTTGTTTTT 58.625 40.909 0.00 0.00 0.00 1.94
47 48 3.032265 AGGCACCTCTCCTTTTGTTTT 57.968 42.857 0.00 0.00 0.00 2.43
48 49 2.755952 AGGCACCTCTCCTTTTGTTT 57.244 45.000 0.00 0.00 0.00 2.83
49 50 2.755952 AAGGCACCTCTCCTTTTGTT 57.244 45.000 0.00 0.00 40.87 2.83
54 55 1.075659 GGCAAAGGCACCTCTCCTT 59.924 57.895 0.00 0.00 45.31 3.36
55 56 1.719063 TTGGCAAAGGCACCTCTCCT 61.719 55.000 0.00 0.00 43.71 3.69
56 57 1.228552 TTGGCAAAGGCACCTCTCC 60.229 57.895 0.00 0.00 43.71 3.71
57 58 1.871126 GCTTGGCAAAGGCACCTCTC 61.871 60.000 2.26 0.00 43.71 3.20
58 59 1.905354 GCTTGGCAAAGGCACCTCT 60.905 57.895 2.26 0.00 43.71 3.69
59 60 2.202395 TGCTTGGCAAAGGCACCTC 61.202 57.895 9.79 0.00 43.71 3.85
60 61 2.123338 TGCTTGGCAAAGGCACCT 60.123 55.556 9.79 0.00 43.71 4.00
86 87 1.705337 CGGGACATGTCATTCGGCAC 61.705 60.000 26.47 7.02 0.00 5.01
87 88 1.449423 CGGGACATGTCATTCGGCA 60.449 57.895 26.47 0.00 0.00 5.69
88 89 2.180204 CCGGGACATGTCATTCGGC 61.180 63.158 28.45 13.16 34.48 5.54
89 90 1.523711 CCCGGGACATGTCATTCGG 60.524 63.158 30.58 30.58 38.20 4.30
107 108 2.765122 AGTTGAGAGCAAAGAGAGTGC 58.235 47.619 0.00 0.00 42.55 4.40
197 198 0.976641 TGAAGCAAGACGAGGGACAT 59.023 50.000 0.00 0.00 0.00 3.06
212 217 1.811266 CTCCACCGCACCGATGAAG 60.811 63.158 0.00 0.00 0.00 3.02
218 223 4.293648 TCACACTCCACCGCACCG 62.294 66.667 0.00 0.00 0.00 4.94
219 224 2.357517 CTCACACTCCACCGCACC 60.358 66.667 0.00 0.00 0.00 5.01
220 225 0.531974 TTTCTCACACTCCACCGCAC 60.532 55.000 0.00 0.00 0.00 5.34
221 226 0.179234 TTTTCTCACACTCCACCGCA 59.821 50.000 0.00 0.00 0.00 5.69
222 227 0.868406 CTTTTCTCACACTCCACCGC 59.132 55.000 0.00 0.00 0.00 5.68
257 262 1.453762 GCTGGAATGCTGGATGGAGC 61.454 60.000 0.00 0.00 39.62 4.70
258 263 1.164662 CGCTGGAATGCTGGATGGAG 61.165 60.000 0.00 0.00 0.00 3.86
259 264 1.153107 CGCTGGAATGCTGGATGGA 60.153 57.895 0.00 0.00 0.00 3.41
260 265 1.033746 AACGCTGGAATGCTGGATGG 61.034 55.000 0.00 0.00 0.00 3.51
261 266 0.813184 AAACGCTGGAATGCTGGATG 59.187 50.000 0.00 0.00 0.00 3.51
320 325 2.729862 CGCGCTGTATACTCCCGC 60.730 66.667 18.64 18.64 41.10 6.13
351 356 1.206578 CGATGTTGAACGGTGTGGC 59.793 57.895 0.00 0.00 0.00 5.01
379 384 2.509561 GGACCGGCGAAAGAGAGC 60.510 66.667 9.30 0.00 0.00 4.09
485 490 1.701847 ACAGTGCCTCTTCTTCCATGT 59.298 47.619 0.00 0.00 0.00 3.21
534 539 2.120232 CATTAACTAGCAGCTCCGTCG 58.880 52.381 0.00 0.00 0.00 5.12
537 542 3.786635 ACTTCATTAACTAGCAGCTCCG 58.213 45.455 0.00 0.00 0.00 4.63
909 918 2.692368 GCCACCATGGGAGGGAGA 60.692 66.667 22.59 0.00 38.19 3.71
910 919 3.016971 TGCCACCATGGGAGGGAG 61.017 66.667 22.59 4.51 38.19 4.30
966 995 1.307097 GGAGTCGTAGTATCGGCAGT 58.693 55.000 0.00 0.00 37.93 4.40
976 1005 1.130749 CCTTCACTCGTGGAGTCGTAG 59.869 57.143 4.74 0.00 41.37 3.51
977 1006 1.162698 CCTTCACTCGTGGAGTCGTA 58.837 55.000 4.74 0.00 41.37 3.43
978 1007 0.822532 ACCTTCACTCGTGGAGTCGT 60.823 55.000 4.74 0.00 41.37 4.34
982 1011 0.811915 ATCGACCTTCACTCGTGGAG 59.188 55.000 0.00 0.00 35.94 3.86
983 1012 0.526211 CATCGACCTTCACTCGTGGA 59.474 55.000 0.00 0.00 32.77 4.02
1171 1213 1.112113 GCTACTACTAGGCTGGTGCA 58.888 55.000 14.37 0.00 41.91 4.57
1179 1221 6.294065 CCGGTTGAAATAGAGCTACTACTAGG 60.294 46.154 0.00 0.00 33.62 3.02
1185 1227 2.500098 TGCCGGTTGAAATAGAGCTACT 59.500 45.455 1.90 0.00 0.00 2.57
1210 1252 3.803082 CCGTCTGTGCCAATGCGG 61.803 66.667 0.00 0.00 41.78 5.69
1211 1253 2.741985 TCCGTCTGTGCCAATGCG 60.742 61.111 0.00 0.00 41.78 4.73
1220 1262 1.070786 ACCAAATGCGTCCGTCTGT 59.929 52.632 0.00 0.00 0.00 3.41
1260 1307 1.375908 GCCTTGTCCATCTGCACGA 60.376 57.895 0.00 0.00 0.00 4.35
1591 1638 1.371558 GTCCAGCTCCAGGACGTTT 59.628 57.895 6.00 0.00 45.35 3.60
1613 1660 3.390521 TCCGGCTTCGTGGCAGAT 61.391 61.111 0.00 0.00 41.89 2.90
1726 1773 1.261938 TGTATCCCTCCACGGTGGTG 61.262 60.000 25.53 22.47 43.99 4.17
1727 1774 0.545787 TTGTATCCCTCCACGGTGGT 60.546 55.000 25.53 9.60 39.03 4.16
1730 1777 1.905512 GCTTGTATCCCTCCACGGT 59.094 57.895 0.00 0.00 0.00 4.83
1902 1977 2.970324 GGCAGGCGAAACGACACA 60.970 61.111 0.00 0.00 37.34 3.72
1929 2004 1.207593 GCTGCTTGCAAGTACACGG 59.792 57.895 26.55 15.77 42.31 4.94
2090 2171 0.106769 TGGGCAGAAGAACACAGCAA 60.107 50.000 0.00 0.00 0.00 3.91
2101 2185 1.207089 CTGAACTACCGATGGGCAGAA 59.793 52.381 0.21 0.00 36.48 3.02
2102 2186 0.824109 CTGAACTACCGATGGGCAGA 59.176 55.000 0.21 0.00 36.48 4.26
2103 2187 0.824109 TCTGAACTACCGATGGGCAG 59.176 55.000 0.00 0.00 36.48 4.85
2243 2331 0.106619 TTTGTTAGGGGCGTGTGGTT 60.107 50.000 0.00 0.00 0.00 3.67
2343 2431 3.939939 TGAGCAGTGAAGCCGCCA 61.940 61.111 0.00 0.00 34.23 5.69
2354 2442 3.136763 AGTGAGTTGTGATTGTGAGCAG 58.863 45.455 0.00 0.00 0.00 4.24
2373 2461 6.420604 CACCTTAAAATTCGCAACATTCAAGT 59.579 34.615 0.00 0.00 0.00 3.16
2460 2549 1.737355 ATAACCACGCATGCATGGCC 61.737 55.000 31.57 11.26 39.84 5.36
2462 2551 2.493035 TCTATAACCACGCATGCATGG 58.507 47.619 30.19 30.19 42.13 3.66
2509 2598 6.207417 CAGGTTAGAAATCAACACCTCAACAT 59.793 38.462 0.00 0.00 35.57 2.71


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

AutoCloner maintained by Alex Coulton.