Multiple sequence alignment - TraesCS2B01G420400

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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 TraesCS2B01G420400 chr2B 100.000 3996 0 0 1 3996 602761399 602765394 0.000000e+00 7380.0
1 TraesCS2B01G420400 chr2B 83.710 221 31 4 2087 2303 54440307 54440526 1.880000e-48 204.0
2 TraesCS2B01G420400 chr2A 91.834 3943 174 64 105 3994 656239010 656242857 0.000000e+00 5361.0
3 TraesCS2B01G420400 chr2D 94.298 3367 108 33 672 3994 512685463 512688789 0.000000e+00 5077.0
4 TraesCS2B01G420400 chr2D 88.491 643 36 16 17 649 512684858 512685472 0.000000e+00 743.0
5 TraesCS2B01G420400 chr1B 92.989 1740 62 12 2261 3951 332586679 332584951 0.000000e+00 2483.0
6 TraesCS2B01G420400 chr6A 94.737 1254 40 5 2280 3510 441441550 441442800 0.000000e+00 1927.0
7 TraesCS2B01G420400 chr6A 78.464 599 95 24 2083 2660 473575567 473574982 1.060000e-95 361.0
8 TraesCS2B01G420400 chr6A 92.339 248 16 2 2280 2527 441443048 441442804 2.290000e-92 350.0
9 TraesCS2B01G420400 chr6A 87.000 200 26 0 2077 2276 500083817 500083618 4.020000e-55 226.0
10 TraesCS2B01G420400 chr6A 83.333 102 12 3 3866 3966 473573758 473573661 5.500000e-14 89.8
11 TraesCS2B01G420400 chr6B 78.523 596 88 26 2083 2654 486224664 486225243 4.910000e-94 355.0
12 TraesCS2B01G420400 chr6B 86.500 200 27 0 2077 2276 539727742 539727543 1.870000e-53 220.0
13 TraesCS2B01G420400 chr6B 83.333 102 12 3 3866 3966 486226492 486226589 5.500000e-14 89.8
14 TraesCS2B01G420400 chr6D 78.203 601 93 26 2083 2660 334227663 334227078 2.290000e-92 350.0
15 TraesCS2B01G420400 chr6D 86.667 195 26 0 2082 2276 358326193 358325999 2.420000e-52 217.0
16 TraesCS2B01G420400 chr6D 79.412 102 11 6 3866 3966 334225830 334225738 3.330000e-06 63.9
17 TraesCS2B01G420400 chr5B 97.143 35 1 0 49 83 685613709 685613675 4.310000e-05 60.2
18 TraesCS2B01G420400 chr1A 97.143 35 1 0 49 83 22485788 22485822 4.310000e-05 60.2


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 TraesCS2B01G420400 chr2B 602761399 602765394 3995 False 7380.00 7380 100.0000 1 3996 1 chr2B.!!$F2 3995
1 TraesCS2B01G420400 chr2A 656239010 656242857 3847 False 5361.00 5361 91.8340 105 3994 1 chr2A.!!$F1 3889
2 TraesCS2B01G420400 chr2D 512684858 512688789 3931 False 2910.00 5077 91.3945 17 3994 2 chr2D.!!$F1 3977
3 TraesCS2B01G420400 chr1B 332584951 332586679 1728 True 2483.00 2483 92.9890 2261 3951 1 chr1B.!!$R1 1690
4 TraesCS2B01G420400 chr6A 441441550 441442800 1250 False 1927.00 1927 94.7370 2280 3510 1 chr6A.!!$F1 1230
5 TraesCS2B01G420400 chr6A 473573661 473575567 1906 True 225.40 361 80.8985 2083 3966 2 chr6A.!!$R3 1883
6 TraesCS2B01G420400 chr6B 486224664 486226589 1925 False 222.40 355 80.9280 2083 3966 2 chr6B.!!$F1 1883
7 TraesCS2B01G420400 chr6D 334225738 334227663 1925 True 206.95 350 78.8075 2083 3966 2 chr6D.!!$R2 1883

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
649 673 0.032217 TGCTCCAAATCCAATCCCCC 60.032 55.0 0.00 0.0 0.00 5.40 F
653 677 0.105504 CCAAATCCAATCCCCCTCCC 60.106 60.0 0.00 0.0 0.00 4.30 F
654 678 0.105504 CAAATCCAATCCCCCTCCCC 60.106 60.0 0.00 0.0 0.00 4.81 F
1138 1167 0.240945 ACGCGCTTTCTTGGATTTGG 59.759 50.0 5.73 0.0 0.00 3.28 F
1510 1573 0.686789 TGATGTGTGGCAGCAGTACT 59.313 50.0 0.00 0.0 38.74 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1943 0.116342 TAGCCCCTGAGGACACAGAA 59.884 55.000 0.00 0.00 39.94 3.02 R
2368 2451 1.079405 CGCCAGCTTCGGGTTCTTA 60.079 57.895 0.00 0.00 0.00 2.10 R
2419 2502 2.672996 CCTTGGTGGTGCGGGAAG 60.673 66.667 0.00 0.00 0.00 3.46 R
2765 2926 2.513026 CTTCCCGACCTGTCCTGCAG 62.513 65.000 6.78 6.78 44.63 4.41 R
3401 3679 0.398696 AGAAACCGCACCACCACATA 59.601 50.000 0.00 0.00 0.00 2.29 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
21 22 4.955811 ATACAAAGGATATCTCGGTGCA 57.044 40.909 2.05 0.00 0.00 4.57
22 23 3.845781 ACAAAGGATATCTCGGTGCAT 57.154 42.857 2.05 0.00 0.00 3.96
32 33 1.134310 TCTCGGTGCATTGCTCATCAT 60.134 47.619 10.49 0.00 0.00 2.45
42 43 7.080099 GTGCATTGCTCATCATATTTCGTATT 58.920 34.615 10.49 0.00 0.00 1.89
46 47 6.785488 TGCTCATCATATTTCGTATTCCAC 57.215 37.500 0.00 0.00 0.00 4.02
53 54 6.392354 TCATATTTCGTATTCCACCGTATCC 58.608 40.000 0.00 0.00 0.00 2.59
56 57 0.313043 CGTATTCCACCGTATCCGCT 59.687 55.000 0.00 0.00 0.00 5.52
64 65 0.178068 ACCGTATCCGCTTGATGCTT 59.822 50.000 0.00 0.00 40.11 3.91
69 70 3.002656 CGTATCCGCTTGATGCTTCATTT 59.997 43.478 2.75 0.00 40.11 2.32
77 78 5.858049 CGCTTGATGCTTCATTTTGAGTTTA 59.142 36.000 2.75 0.00 40.11 2.01
86 87 7.865385 TGCTTCATTTTGAGTTTATAAAAGCGT 59.135 29.630 0.00 0.00 0.00 5.07
88 89 8.736751 TTCATTTTGAGTTTATAAAAGCGTCC 57.263 30.769 0.00 0.00 0.00 4.79
89 90 8.106247 TCATTTTGAGTTTATAAAAGCGTCCT 57.894 30.769 0.00 0.00 0.00 3.85
90 91 8.234546 TCATTTTGAGTTTATAAAAGCGTCCTC 58.765 33.333 0.00 2.31 0.00 3.71
91 92 7.739498 TTTTGAGTTTATAAAAGCGTCCTCT 57.261 32.000 0.00 0.00 0.00 3.69
92 93 8.836268 TTTTGAGTTTATAAAAGCGTCCTCTA 57.164 30.769 0.00 0.00 0.00 2.43
93 94 9.444600 TTTTGAGTTTATAAAAGCGTCCTCTAT 57.555 29.630 0.00 0.00 0.00 1.98
130 133 8.270799 GCACATATATTGTCATGCATTTTGTTC 58.729 33.333 0.00 0.00 36.00 3.18
144 147 8.020861 TGCATTTTGTTCTGAAGCAATATTTC 57.979 30.769 0.00 0.00 0.00 2.17
197 200 5.897377 AGGCCATATTTTGAACTGTACAC 57.103 39.130 5.01 0.00 0.00 2.90
198 201 4.394920 AGGCCATATTTTGAACTGTACACG 59.605 41.667 5.01 0.00 0.00 4.49
199 202 4.393680 GGCCATATTTTGAACTGTACACGA 59.606 41.667 0.00 0.00 0.00 4.35
200 203 5.447279 GGCCATATTTTGAACTGTACACGAG 60.447 44.000 0.00 0.00 0.00 4.18
230 233 6.416750 CACGCCTTAAAAGTTAAAACTCTTGG 59.583 38.462 0.00 0.00 38.57 3.61
261 264 1.548973 GCCAGTGTCGACGACAACAG 61.549 60.000 30.68 21.53 44.49 3.16
272 275 1.764134 ACGACAACAGGACTTGGGTAA 59.236 47.619 0.00 0.00 0.00 2.85
273 276 2.370849 ACGACAACAGGACTTGGGTAAT 59.629 45.455 0.00 0.00 0.00 1.89
274 277 2.742053 CGACAACAGGACTTGGGTAATG 59.258 50.000 0.00 0.00 0.00 1.90
275 278 3.081804 GACAACAGGACTTGGGTAATGG 58.918 50.000 0.00 0.00 0.00 3.16
276 279 2.225017 ACAACAGGACTTGGGTAATGGG 60.225 50.000 0.00 0.00 0.00 4.00
277 280 1.755200 ACAGGACTTGGGTAATGGGT 58.245 50.000 0.00 0.00 0.00 4.51
278 281 2.923908 ACAGGACTTGGGTAATGGGTA 58.076 47.619 0.00 0.00 0.00 3.69
279 282 2.844348 ACAGGACTTGGGTAATGGGTAG 59.156 50.000 0.00 0.00 0.00 3.18
280 283 2.844348 CAGGACTTGGGTAATGGGTAGT 59.156 50.000 0.00 0.00 0.00 2.73
317 320 4.634991 GTTGAAACGAATTACGCTGTAGG 58.365 43.478 0.00 0.00 46.94 3.18
391 399 2.689553 AAAAGGTTGCACCAAACAGG 57.310 45.000 7.86 0.00 41.95 4.00
552 567 4.200283 CCGACTCCTCGCAGCCTC 62.200 72.222 0.00 0.00 38.70 4.70
553 568 4.200283 CGACTCCTCGCAGCCTCC 62.200 72.222 0.00 0.00 31.91 4.30
580 595 1.646189 GATCGAGCAAGAACACCTCC 58.354 55.000 0.00 0.00 0.00 4.30
594 609 2.285442 CTCCCGACCCCCTTCCTT 60.285 66.667 0.00 0.00 0.00 3.36
595 610 2.285144 TCCCGACCCCCTTCCTTC 60.285 66.667 0.00 0.00 0.00 3.46
596 611 3.408853 CCCGACCCCCTTCCTTCC 61.409 72.222 0.00 0.00 0.00 3.46
597 612 2.285442 CCGACCCCCTTCCTTCCT 60.285 66.667 0.00 0.00 0.00 3.36
617 641 2.202440 CCCTCACAGTACGTCGCG 60.202 66.667 0.00 0.00 0.00 5.87
644 668 3.675348 TCCATCTGCTCCAAATCCAAT 57.325 42.857 0.00 0.00 0.00 3.16
645 669 3.559069 TCCATCTGCTCCAAATCCAATC 58.441 45.455 0.00 0.00 0.00 2.67
646 670 2.626743 CCATCTGCTCCAAATCCAATCC 59.373 50.000 0.00 0.00 0.00 3.01
647 671 2.442236 TCTGCTCCAAATCCAATCCC 57.558 50.000 0.00 0.00 0.00 3.85
648 672 1.063717 TCTGCTCCAAATCCAATCCCC 60.064 52.381 0.00 0.00 0.00 4.81
649 673 0.032217 TGCTCCAAATCCAATCCCCC 60.032 55.000 0.00 0.00 0.00 5.40
650 674 0.262876 GCTCCAAATCCAATCCCCCT 59.737 55.000 0.00 0.00 0.00 4.79
651 675 1.755621 GCTCCAAATCCAATCCCCCTC 60.756 57.143 0.00 0.00 0.00 4.30
652 676 0.933700 TCCAAATCCAATCCCCCTCC 59.066 55.000 0.00 0.00 0.00 4.30
653 677 0.105504 CCAAATCCAATCCCCCTCCC 60.106 60.000 0.00 0.00 0.00 4.30
654 678 0.105504 CAAATCCAATCCCCCTCCCC 60.106 60.000 0.00 0.00 0.00 4.81
655 679 0.254784 AAATCCAATCCCCCTCCCCT 60.255 55.000 0.00 0.00 0.00 4.79
656 680 0.702706 AATCCAATCCCCCTCCCCTC 60.703 60.000 0.00 0.00 0.00 4.30
657 681 2.661292 ATCCAATCCCCCTCCCCTCC 62.661 65.000 0.00 0.00 0.00 4.30
658 682 2.778717 CAATCCCCCTCCCCTCCC 60.779 72.222 0.00 0.00 0.00 4.30
659 683 4.138815 AATCCCCCTCCCCTCCCC 62.139 72.222 0.00 0.00 0.00 4.81
664 688 4.516326 CCCTCCCCTCCCCGGAAT 62.516 72.222 0.73 0.00 33.16 3.01
665 689 2.849646 CCTCCCCTCCCCGGAATC 60.850 72.222 0.73 0.00 33.16 2.52
666 690 2.849646 CTCCCCTCCCCGGAATCC 60.850 72.222 0.73 0.00 33.16 3.01
667 691 4.509412 TCCCCTCCCCGGAATCCC 62.509 72.222 0.73 0.00 33.16 3.85
882 908 2.464865 CTCCGCTCAAGAAATCTACCG 58.535 52.381 0.00 0.00 0.00 4.02
889 915 4.253685 CTCAAGAAATCTACCGGAAGCAA 58.746 43.478 9.46 0.00 0.00 3.91
890 916 4.253685 TCAAGAAATCTACCGGAAGCAAG 58.746 43.478 9.46 0.00 0.00 4.01
891 917 2.633488 AGAAATCTACCGGAAGCAAGC 58.367 47.619 9.46 0.00 0.00 4.01
892 918 2.027192 AGAAATCTACCGGAAGCAAGCA 60.027 45.455 9.46 0.00 0.00 3.91
897 923 0.955428 TACCGGAAGCAAGCAAGCAG 60.955 55.000 9.46 0.00 36.85 4.24
898 924 2.126580 CGGAAGCAAGCAAGCAGC 60.127 61.111 3.19 0.00 46.19 5.25
940 969 2.341101 GCCGTCGTCTTCCTCCTCA 61.341 63.158 0.00 0.00 0.00 3.86
946 975 3.607310 CGTCGTCTTCCTCCTCATATTCG 60.607 52.174 0.00 0.00 0.00 3.34
949 978 3.304794 CGTCTTCCTCCTCATATTCGGAC 60.305 52.174 0.00 0.00 0.00 4.79
950 979 3.637229 GTCTTCCTCCTCATATTCGGACA 59.363 47.826 0.00 0.00 0.00 4.02
985 1014 0.324943 GTTTGAGAGGTAGCCTGGCA 59.675 55.000 22.65 3.92 31.76 4.92
1039 1068 3.814316 GCCCCAGGTAAATCTCTTTGTGT 60.814 47.826 0.00 0.00 0.00 3.72
1068 1097 5.006386 TGGCTTTTCTTCTCCTTGATCTTC 58.994 41.667 0.00 0.00 0.00 2.87
1107 1136 4.019858 CTCCTCTCTGTGACATGGTTCTA 58.980 47.826 0.00 0.00 0.00 2.10
1108 1137 4.019858 TCCTCTCTGTGACATGGTTCTAG 58.980 47.826 0.00 0.00 0.00 2.43
1109 1138 3.430098 CCTCTCTGTGACATGGTTCTAGC 60.430 52.174 0.00 0.00 0.00 3.42
1110 1139 3.435275 TCTCTGTGACATGGTTCTAGCT 58.565 45.455 0.00 0.00 0.00 3.32
1119 1148 0.472044 TGGTTCTAGCTTGGTGTGCA 59.528 50.000 0.00 0.00 0.00 4.57
1130 1159 2.327940 GTGTGCACGCGCTTTCTT 59.672 55.556 15.68 0.00 39.64 2.52
1131 1160 2.005537 GTGTGCACGCGCTTTCTTG 61.006 57.895 15.68 0.00 39.64 3.02
1135 1164 1.210155 GCACGCGCTTTCTTGGATT 59.790 52.632 5.73 0.00 34.30 3.01
1136 1165 0.387239 GCACGCGCTTTCTTGGATTT 60.387 50.000 5.73 0.00 34.30 2.17
1138 1167 0.240945 ACGCGCTTTCTTGGATTTGG 59.759 50.000 5.73 0.00 0.00 3.28
1139 1168 1.072666 CGCGCTTTCTTGGATTTGGC 61.073 55.000 5.56 0.00 0.00 4.52
1154 1183 1.600058 TTGGCCATGATCTCCCTCTT 58.400 50.000 6.09 0.00 0.00 2.85
1155 1184 1.600058 TGGCCATGATCTCCCTCTTT 58.400 50.000 0.00 0.00 0.00 2.52
1156 1185 1.213678 TGGCCATGATCTCCCTCTTTG 59.786 52.381 0.00 0.00 0.00 2.77
1157 1186 1.213926 GGCCATGATCTCCCTCTTTGT 59.786 52.381 0.00 0.00 0.00 2.83
1158 1187 2.295885 GCCATGATCTCCCTCTTTGTG 58.704 52.381 0.00 0.00 0.00 3.33
1159 1188 2.928334 CCATGATCTCCCTCTTTGTGG 58.072 52.381 0.00 0.00 0.00 4.17
1168 1197 0.768622 CCTCTTTGTGGGTGTGGGTA 59.231 55.000 0.00 0.00 0.00 3.69
1175 1212 0.831307 GTGGGTGTGGGTATCCTCTC 59.169 60.000 0.00 0.00 0.00 3.20
1245 1282 1.966762 CAACACAATCAGCACCCCC 59.033 57.895 0.00 0.00 0.00 5.40
1306 1355 1.303309 CCTGCGGCTTTAATCCTCTG 58.697 55.000 0.00 0.00 0.00 3.35
1359 1412 1.880027 ACGCACCATCACCTTTCTTTC 59.120 47.619 0.00 0.00 0.00 2.62
1510 1573 0.686789 TGATGTGTGGCAGCAGTACT 59.313 50.000 0.00 0.00 38.74 2.73
1576 1639 4.137543 GGTGGTGTGTTTCTCTTTCATCT 58.862 43.478 0.00 0.00 0.00 2.90
1619 1682 2.698274 TCACCTTTTCCTTTGCCTTTCC 59.302 45.455 0.00 0.00 0.00 3.13
1620 1683 2.700371 CACCTTTTCCTTTGCCTTTCCT 59.300 45.455 0.00 0.00 0.00 3.36
1621 1684 2.700371 ACCTTTTCCTTTGCCTTTCCTG 59.300 45.455 0.00 0.00 0.00 3.86
1622 1685 2.548707 CCTTTTCCTTTGCCTTTCCTGC 60.549 50.000 0.00 0.00 0.00 4.85
1623 1686 2.086610 TTTCCTTTGCCTTTCCTGCT 57.913 45.000 0.00 0.00 0.00 4.24
1663 1728 4.864704 TTGTATCCTTTTGCTTGGTTCC 57.135 40.909 0.00 0.00 0.00 3.62
1689 1754 2.560981 TGCACCGTAGAGATTCTTGACA 59.439 45.455 0.00 0.00 0.00 3.58
1873 1941 3.686241 CAAGTGCTGCACTATGTGTGTAT 59.314 43.478 33.11 13.38 44.62 2.29
1874 1942 3.935203 AAGTGCTGCACTATGTGTGTATC 59.065 43.478 33.11 2.79 44.62 2.24
1875 1943 4.323028 AAGTGCTGCACTATGTGTGTATCT 60.323 41.667 33.11 12.13 44.62 1.98
2293 2361 3.304764 CTCTTCGTCGTCGTCCGCA 62.305 63.158 1.33 0.00 38.33 5.69
2351 2434 2.158959 GTCGCGAACTCGTCCATGG 61.159 63.158 12.06 4.97 42.22 3.66
2419 2502 2.432628 CACGACCTGAACCTCGCC 60.433 66.667 0.00 0.00 32.98 5.54
3130 3366 7.095183 AGATGGTGGATATGGTGTTTGATAT 57.905 36.000 0.00 0.00 0.00 1.63
3131 3367 7.170965 AGATGGTGGATATGGTGTTTGATATC 58.829 38.462 0.00 0.00 32.77 1.63
3132 3368 6.514012 TGGTGGATATGGTGTTTGATATCT 57.486 37.500 3.98 0.00 33.67 1.98
3133 3369 6.910191 TGGTGGATATGGTGTTTGATATCTT 58.090 36.000 3.98 0.00 33.67 2.40
3168 3425 6.927294 TTCTTTCTTTCTGGTGTTCTTCTC 57.073 37.500 0.00 0.00 0.00 2.87
3170 3427 6.653989 TCTTTCTTTCTGGTGTTCTTCTCTT 58.346 36.000 0.00 0.00 0.00 2.85
3171 3428 6.763610 TCTTTCTTTCTGGTGTTCTTCTCTTC 59.236 38.462 0.00 0.00 0.00 2.87
3172 3429 5.878406 TCTTTCTGGTGTTCTTCTCTTCT 57.122 39.130 0.00 0.00 0.00 2.85
3183 3440 6.645003 GTGTTCTTCTCTTCTTCTTCTTCCTC 59.355 42.308 0.00 0.00 0.00 3.71
3317 3591 4.080695 CCATGGATGGTGCTATATGCTAGT 60.081 45.833 5.56 0.00 43.05 2.57
3401 3679 1.402968 CCAGTACTACGTACATGGCGT 59.597 52.381 18.69 18.69 41.03 5.68
3546 3889 2.807967 TCAGCTTTGTGTGTAGATGCAC 59.192 45.455 0.00 0.00 39.65 4.57
3602 3947 9.286946 GTAGTAGTAGCATGTAACTTTGTACTG 57.713 37.037 7.29 0.00 0.00 2.74
3659 4004 9.979270 GAGTACAAGTATCATCATCTTTGTTTG 57.021 33.333 0.00 0.00 0.00 2.93
3734 4095 4.096081 GCTCATCCAAAGTTGATCAGAAGG 59.904 45.833 0.00 0.00 0.00 3.46
3781 4142 5.139727 AGTGTCCTTCAATGTCATTTCCAA 58.860 37.500 0.00 0.00 0.00 3.53
3853 4435 6.672266 TTGTCTTTCTATCTGTCACCTCTT 57.328 37.500 0.00 0.00 0.00 2.85
3854 4436 6.030548 TGTCTTTCTATCTGTCACCTCTTG 57.969 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.955811 TGCACCGAGATATCCTTTGTAT 57.044 40.909 0.00 0.00 0.00 2.29
1 2 4.955811 ATGCACCGAGATATCCTTTGTA 57.044 40.909 0.00 0.00 0.00 2.41
2 3 3.845781 ATGCACCGAGATATCCTTTGT 57.154 42.857 0.00 0.00 0.00 2.83
3 4 3.304257 GCAATGCACCGAGATATCCTTTG 60.304 47.826 0.00 0.00 0.00 2.77
4 5 2.880890 GCAATGCACCGAGATATCCTTT 59.119 45.455 0.00 0.00 0.00 3.11
5 6 2.105477 AGCAATGCACCGAGATATCCTT 59.895 45.455 8.35 0.00 0.00 3.36
6 7 1.696336 AGCAATGCACCGAGATATCCT 59.304 47.619 8.35 0.00 0.00 3.24
7 8 2.072298 GAGCAATGCACCGAGATATCC 58.928 52.381 8.35 0.00 0.00 2.59
8 9 2.759191 TGAGCAATGCACCGAGATATC 58.241 47.619 8.35 0.00 0.00 1.63
9 10 2.916702 TGAGCAATGCACCGAGATAT 57.083 45.000 8.35 0.00 0.00 1.63
10 11 2.102925 TGATGAGCAATGCACCGAGATA 59.897 45.455 8.35 0.00 0.00 1.98
11 12 1.134310 TGATGAGCAATGCACCGAGAT 60.134 47.619 8.35 0.00 0.00 2.75
12 13 0.249955 TGATGAGCAATGCACCGAGA 59.750 50.000 8.35 0.00 0.00 4.04
13 14 1.306148 ATGATGAGCAATGCACCGAG 58.694 50.000 8.35 0.00 0.00 4.63
14 15 2.618442 TATGATGAGCAATGCACCGA 57.382 45.000 8.35 0.00 0.00 4.69
15 16 3.909776 AATATGATGAGCAATGCACCG 57.090 42.857 8.35 0.00 0.00 4.94
16 17 4.224433 CGAAATATGATGAGCAATGCACC 58.776 43.478 8.35 0.00 0.00 5.01
17 18 4.852138 ACGAAATATGATGAGCAATGCAC 58.148 39.130 8.35 0.73 0.00 4.57
18 19 6.806388 ATACGAAATATGATGAGCAATGCA 57.194 33.333 8.35 0.00 0.00 3.96
19 20 6.744537 GGAATACGAAATATGATGAGCAATGC 59.255 38.462 0.00 0.00 0.00 3.56
20 21 7.747799 GTGGAATACGAAATATGATGAGCAATG 59.252 37.037 0.00 0.00 0.00 2.82
21 22 7.094634 GGTGGAATACGAAATATGATGAGCAAT 60.095 37.037 0.00 0.00 0.00 3.56
22 23 6.204688 GGTGGAATACGAAATATGATGAGCAA 59.795 38.462 0.00 0.00 0.00 3.91
64 65 8.106247 AGGACGCTTTTATAAACTCAAAATGA 57.894 30.769 0.00 0.00 0.00 2.57
101 104 4.103013 TGCATGACAATATATGTGCCCT 57.897 40.909 0.00 0.00 44.12 5.19
102 105 5.395682 AATGCATGACAATATATGTGCCC 57.604 39.130 0.00 0.00 44.12 5.36
107 110 9.738832 TCAGAACAAAATGCATGACAATATATG 57.261 29.630 0.00 0.00 0.00 1.78
116 119 4.587584 TGCTTCAGAACAAAATGCATGA 57.412 36.364 0.00 0.00 0.00 3.07
130 133 7.518161 TGAAGTGTTACGAAATATTGCTTCAG 58.482 34.615 0.00 0.00 36.10 3.02
218 221 6.639279 GCTACAAAATTCGCCAAGAGTTTTAA 59.361 34.615 2.01 0.00 43.82 1.52
230 233 2.724839 CGACACTGGCTACAAAATTCGC 60.725 50.000 0.00 0.00 0.00 4.70
261 264 3.680754 CGAACTACCCATTACCCAAGTCC 60.681 52.174 0.00 0.00 0.00 3.85
272 275 1.895238 CACCGACCGAACTACCCAT 59.105 57.895 0.00 0.00 0.00 4.00
273 276 2.934570 GCACCGACCGAACTACCCA 61.935 63.158 0.00 0.00 0.00 4.51
274 277 2.125793 GCACCGACCGAACTACCC 60.126 66.667 0.00 0.00 0.00 3.69
275 278 2.505557 CGCACCGACCGAACTACC 60.506 66.667 0.00 0.00 0.00 3.18
276 279 2.505557 CCGCACCGACCGAACTAC 60.506 66.667 0.00 0.00 0.00 2.73
277 280 4.424566 GCCGCACCGACCGAACTA 62.425 66.667 0.00 0.00 0.00 2.24
317 320 1.683385 ACCTGCCTCTTTGTTTTCAGC 59.317 47.619 0.00 0.00 0.00 4.26
391 399 0.544697 TCTAAATTCCCTGGGCGTCC 59.455 55.000 8.22 0.00 0.00 4.79
580 595 2.285442 AGGAAGGAAGGGGGTCGG 60.285 66.667 0.00 0.00 0.00 4.79
594 609 1.000019 CGTACTGTGAGGGGGAGGA 60.000 63.158 0.00 0.00 0.00 3.71
595 610 1.305046 ACGTACTGTGAGGGGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
596 611 1.654954 CGACGTACTGTGAGGGGGAG 61.655 65.000 0.00 0.00 0.00 4.30
597 612 1.676635 CGACGTACTGTGAGGGGGA 60.677 63.158 0.00 0.00 0.00 4.81
617 641 0.034476 TGGAGCAGATGGATCGATGC 59.966 55.000 10.37 10.37 38.97 3.91
647 671 4.516326 ATTCCGGGGAGGGGAGGG 62.516 72.222 0.00 0.00 41.52 4.30
648 672 2.849646 GATTCCGGGGAGGGGAGG 60.850 72.222 0.00 0.00 41.52 4.30
649 673 2.849646 GGATTCCGGGGAGGGGAG 60.850 72.222 0.00 0.00 41.52 4.30
650 674 4.509412 GGGATTCCGGGGAGGGGA 62.509 72.222 0.00 0.00 41.52 4.81
667 691 4.825679 GTGAGGGGAGGGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
668 692 4.825679 GGTGAGGGGAGGGGAGGG 62.826 77.778 0.00 0.00 0.00 4.30
670 694 4.075793 TCGGTGAGGGGAGGGGAG 62.076 72.222 0.00 0.00 0.00 4.30
778 802 2.482721 CGCTCTTCCCACATACGTTTTT 59.517 45.455 0.00 0.00 0.00 1.94
882 908 0.666577 CTTGCTGCTTGCTTGCTTCC 60.667 55.000 0.00 0.00 43.37 3.46
946 975 1.672881 CAATTCTTGCTCCGGATGTCC 59.327 52.381 3.57 0.00 0.00 4.02
949 978 3.191162 TCAAACAATTCTTGCTCCGGATG 59.809 43.478 3.57 0.00 0.00 3.51
950 979 3.420893 TCAAACAATTCTTGCTCCGGAT 58.579 40.909 3.57 0.00 0.00 4.18
971 1000 0.257039 CCAATTGCCAGGCTACCTCT 59.743 55.000 14.15 0.00 0.00 3.69
985 1014 0.034186 TCCATGCGAAGGCTCCAATT 60.034 50.000 0.00 0.00 40.82 2.32
1039 1068 5.598005 TCAAGGAGAAGAAAAGCCAAATTCA 59.402 36.000 0.00 0.00 0.00 2.57
1068 1097 0.460987 GAGGATGAACAGACAGCGGG 60.461 60.000 0.00 0.00 0.00 6.13
1109 1138 3.468266 AAAGCGCGTGCACACCAAG 62.468 57.895 24.79 0.39 46.23 3.61
1110 1139 3.462333 GAAAGCGCGTGCACACCAA 62.462 57.895 24.79 0.00 46.23 3.67
1119 1148 0.240945 CCAAATCCAAGAAAGCGCGT 59.759 50.000 8.43 0.00 0.00 6.01
1130 1159 1.133388 GGGAGATCATGGCCAAATCCA 60.133 52.381 21.77 2.06 40.97 3.41
1131 1160 1.146566 AGGGAGATCATGGCCAAATCC 59.853 52.381 21.77 17.78 0.00 3.01
1135 1164 1.600058 AAGAGGGAGATCATGGCCAA 58.400 50.000 10.96 0.00 0.00 4.52
1136 1165 1.213678 CAAAGAGGGAGATCATGGCCA 59.786 52.381 8.56 8.56 0.00 5.36
1138 1167 2.295885 CACAAAGAGGGAGATCATGGC 58.704 52.381 0.00 0.00 0.00 4.40
1139 1168 2.928334 CCACAAAGAGGGAGATCATGG 58.072 52.381 0.00 0.00 0.00 3.66
1154 1183 0.988832 GAGGATACCCACACCCACAA 59.011 55.000 0.00 0.00 33.88 3.33
1155 1184 0.118346 AGAGGATACCCACACCCACA 59.882 55.000 0.00 0.00 33.88 4.17
1156 1185 0.831307 GAGAGGATACCCACACCCAC 59.169 60.000 0.00 0.00 33.88 4.61
1157 1186 0.686441 CGAGAGGATACCCACACCCA 60.686 60.000 0.00 0.00 33.88 4.51
1158 1187 2.125178 CGAGAGGATACCCACACCC 58.875 63.158 0.00 0.00 33.88 4.61
1175 1212 2.443887 TAAAGGAAGAACACGACCCG 57.556 50.000 0.00 0.00 0.00 5.28
1245 1282 5.221621 CCTTAAAGCCTATGGAGAAGAGAGG 60.222 48.000 0.00 0.00 0.00 3.69
1306 1355 2.432174 AAAAGGGGAGGGCAGCAGAC 62.432 60.000 0.00 0.00 0.00 3.51
1359 1412 1.149986 GGGGGATTAGAAAGAGGGGG 58.850 60.000 0.00 0.00 0.00 5.40
1510 1573 3.472652 CTTGTGCTGTTGTAGGGTTGTA 58.527 45.455 0.00 0.00 0.00 2.41
1576 1639 1.076014 GGGCCGGGGAAGAAGAAAA 59.924 57.895 2.18 0.00 0.00 2.29
1619 1682 1.540797 GGAGATTAGAGGCAGCAGCAG 60.541 57.143 2.65 0.00 44.61 4.24
1620 1683 0.467384 GGAGATTAGAGGCAGCAGCA 59.533 55.000 2.65 0.00 44.61 4.41
1621 1684 0.250252 GGGAGATTAGAGGCAGCAGC 60.250 60.000 0.00 0.00 41.10 5.25
1622 1685 1.422531 AGGGAGATTAGAGGCAGCAG 58.577 55.000 0.00 0.00 0.00 4.24
1623 1686 1.885049 AAGGGAGATTAGAGGCAGCA 58.115 50.000 0.00 0.00 0.00 4.41
1663 1728 4.640789 AGAATCTCTACGGTGCAACTAG 57.359 45.455 0.00 0.87 36.74 2.57
1706 1772 2.040606 GTGGAGGTGGGGAGGCTA 59.959 66.667 0.00 0.00 0.00 3.93
1873 1941 1.194781 GCCCCTGAGGACACAGAAGA 61.195 60.000 0.00 0.00 39.94 2.87
1874 1942 1.197430 AGCCCCTGAGGACACAGAAG 61.197 60.000 0.00 0.00 39.94 2.85
1875 1943 0.116342 TAGCCCCTGAGGACACAGAA 59.884 55.000 0.00 0.00 39.94 3.02
2293 2361 4.537433 GCTGAAGCGGAGGCGGAT 62.537 66.667 0.00 0.00 46.35 4.18
2368 2451 1.079405 CGCCAGCTTCGGGTTCTTA 60.079 57.895 0.00 0.00 0.00 2.10
2419 2502 2.672996 CCTTGGTGGTGCGGGAAG 60.673 66.667 0.00 0.00 0.00 3.46
2506 2595 4.534141 CCATTGCCCGCCATTGCC 62.534 66.667 0.00 0.00 0.00 4.52
2765 2926 2.513026 CTTCCCGACCTGTCCTGCAG 62.513 65.000 6.78 6.78 44.63 4.41
3132 3368 9.860898 CCAGAAAGAAAGAAAGAAAGAAAGAAA 57.139 29.630 0.00 0.00 0.00 2.52
3133 3369 9.025041 ACCAGAAAGAAAGAAAGAAAGAAAGAA 57.975 29.630 0.00 0.00 0.00 2.52
3168 3425 5.121454 CACAATTCCGAGGAAGAAGAAGAAG 59.879 44.000 10.56 0.00 37.56 2.85
3170 3427 4.569943 CACAATTCCGAGGAAGAAGAAGA 58.430 43.478 10.56 0.00 37.56 2.87
3171 3428 3.126000 GCACAATTCCGAGGAAGAAGAAG 59.874 47.826 10.56 0.28 37.56 2.85
3172 3429 3.074412 GCACAATTCCGAGGAAGAAGAA 58.926 45.455 10.56 0.00 37.56 2.52
3183 3440 0.460284 ACGGCTAGAGCACAATTCCG 60.460 55.000 3.54 0.00 44.36 4.30
3305 3579 4.683781 GCTTCACACAGACTAGCATATAGC 59.316 45.833 0.00 0.00 46.19 2.97
3307 3581 6.096846 TGAAGCTTCACACAGACTAGCATATA 59.903 38.462 25.16 0.00 33.43 0.86
3317 3591 4.216257 GCCTAAAATGAAGCTTCACACAGA 59.784 41.667 30.66 14.19 40.49 3.41
3401 3679 0.398696 AGAAACCGCACCACCACATA 59.601 50.000 0.00 0.00 0.00 2.29
3546 3889 2.742372 CTCGGTCCCCAAACGCTG 60.742 66.667 0.00 0.00 0.00 5.18
3781 4142 8.985315 ATGTACACCAATATCATCAGTTCAAT 57.015 30.769 0.00 0.00 0.00 2.57
3853 4435 1.331214 CAAGAAAAAGGAGGGCAGCA 58.669 50.000 0.00 0.00 0.00 4.41
3854 4436 1.332195 ACAAGAAAAAGGAGGGCAGC 58.668 50.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.