Multiple sequence alignment - TraesCS3A01G096400

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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 TraesCS3A01G096400 chr3A 100.000 2519 0 0 1 2519 61438828 61436310 0.000000e+00 4652.0
1 TraesCS3A01G096400 chr3A 80.753 1408 208 30 164 1525 103017869 103019259 0.000000e+00 1040.0
2 TraesCS3A01G096400 chr3A 98.182 55 0 1 33 86 733717080 733717026 7.420000e-16 95.3
3 TraesCS3A01G096400 chr3B 92.777 983 32 10 570 1528 78523577 78522610 0.000000e+00 1386.0
4 TraesCS3A01G096400 chr3B 90.430 512 14 5 89 574 78524102 78523600 2.110000e-180 641.0
5 TraesCS3A01G096400 chr3B 90.647 278 15 8 1533 1803 78522523 78522250 2.380000e-95 359.0
6 TraesCS3A01G096400 chr3B 92.444 225 5 5 1784 1996 78522067 78521843 6.770000e-81 311.0
7 TraesCS3A01G096400 chr3B 93.103 87 1 3 2435 2519 78521717 78521634 3.400000e-24 122.0
8 TraesCS3A01G096400 chr3B 84.314 102 11 4 1645 1742 778627432 778627332 7.420000e-16 95.3
9 TraesCS3A01G096400 chr3B 85.227 88 9 3 1 86 462023543 462023458 1.240000e-13 87.9
10 TraesCS3A01G096400 chr3B 82.353 85 11 3 1 83 442080071 442079989 1.250000e-08 71.3
11 TraesCS3A01G096400 chr3D 94.753 667 19 7 1784 2435 48869443 48868778 0.000000e+00 1024.0
12 TraesCS3A01G096400 chr3D 97.254 437 11 1 815 1251 48870658 48870223 0.000000e+00 739.0
13 TraesCS3A01G096400 chr3D 93.439 442 6 5 142 574 48882718 48882291 3.540000e-178 634.0
14 TraesCS3A01G096400 chr3D 95.582 249 10 1 570 817 48882268 48882020 5.050000e-107 398.0
15 TraesCS3A01G096400 chr3D 92.913 254 6 5 1533 1781 48869898 48869652 2.380000e-95 359.0
16 TraesCS3A01G096400 chr3D 91.057 246 4 2 1287 1523 48870226 48869990 1.450000e-82 316.0
17 TraesCS3A01G096400 chr3D 96.512 86 1 2 2436 2519 48868422 48868337 9.390000e-30 141.0
18 TraesCS3A01G096400 chr2D 78.695 1333 220 33 240 1525 1624492 1623177 0.000000e+00 830.0
19 TraesCS3A01G096400 chr2D 78.371 1031 177 32 319 1325 1621212 1622220 5.920000e-176 627.0
20 TraesCS3A01G096400 chr2D 80.355 733 128 12 605 1330 1818162 1817439 2.200000e-150 542.0
21 TraesCS3A01G096400 chr2D 82.609 207 22 11 1562 1768 648871269 648871077 1.200000e-38 171.0
22 TraesCS3A01G096400 chr2B 79.665 954 154 24 577 1522 10215138 10216059 0.000000e+00 651.0
23 TraesCS3A01G096400 chr2B 79.918 244 38 5 238 470 319359804 319360047 4.310000e-38 169.0
24 TraesCS3A01G096400 chr2B 82.353 102 13 4 1645 1742 786389645 786389745 1.610000e-12 84.2
25 TraesCS3A01G096400 chr4D 94.236 399 13 4 1784 2173 141360876 141360479 3.590000e-168 601.0
26 TraesCS3A01G096400 chr4D 88.803 259 15 7 1551 1803 141361310 141361060 3.150000e-79 305.0
27 TraesCS3A01G096400 chr4D 82.828 99 10 5 1 97 80986943 80987036 5.780000e-12 82.4
28 TraesCS3A01G096400 chr2A 80.505 713 126 12 622 1327 708027 708733 3.690000e-148 534.0
29 TraesCS3A01G096400 chr2A 80.365 713 127 12 622 1327 702456 703162 1.720000e-146 529.0
30 TraesCS3A01G096400 chr2A 98.113 53 1 0 33 85 193748115 193748167 2.670000e-15 93.5
31 TraesCS3A01G096400 chr2A 79.518 83 14 3 1 82 696244990 696244910 3.500000e-04 56.5
32 TraesCS3A01G096400 chr6A 100.000 51 0 0 33 83 579381889 579381939 7.420000e-16 95.3
33 TraesCS3A01G096400 chr7A 96.429 56 1 1 33 87 592953001 592952946 9.600000e-15 91.6
34 TraesCS3A01G096400 chr7A 86.585 82 1 1 2 83 111837216 111837145 5.780000e-12 82.4
35 TraesCS3A01G096400 chr5A 96.429 56 1 1 33 87 59982613 59982558 9.600000e-15 91.6
36 TraesCS3A01G096400 chr5A 96.429 56 1 1 33 87 247446476 247446531 9.600000e-15 91.6
37 TraesCS3A01G096400 chr5A 81.481 81 8 4 7 84 536254808 536254732 2.710000e-05 60.2
38 TraesCS3A01G096400 chr4A 96.429 56 1 1 33 87 140107836 140107781 9.600000e-15 91.6
39 TraesCS3A01G096400 chr1A 96.429 56 1 1 33 87 303582852 303582907 9.600000e-15 91.6
40 TraesCS3A01G096400 chr1A 96.429 56 1 1 33 87 450992627 450992682 9.600000e-15 91.6
41 TraesCS3A01G096400 chr7B 83.333 102 12 4 1645 1742 688412980 688413080 3.450000e-14 89.8
42 TraesCS3A01G096400 chr6B 83.333 102 12 4 1645 1742 692624781 692624881 3.450000e-14 89.8
43 TraesCS3A01G096400 chr1B 81.553 103 14 4 1645 1743 39180949 39180848 2.080000e-11 80.5
44 TraesCS3A01G096400 chr6D 94.118 51 3 0 33 83 23781233 23781283 7.470000e-11 78.7


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 TraesCS3A01G096400 chr3A 61436310 61438828 2518 True 4652.0 4652 100.0000 1 2519 1 chr3A.!!$R1 2518
1 TraesCS3A01G096400 chr3A 103017869 103019259 1390 False 1040.0 1040 80.7530 164 1525 1 chr3A.!!$F1 1361
2 TraesCS3A01G096400 chr3B 78521634 78524102 2468 True 563.8 1386 91.8802 89 2519 5 chr3B.!!$R4 2430
3 TraesCS3A01G096400 chr3D 48882020 48882718 698 True 516.0 634 94.5105 142 817 2 chr3D.!!$R2 675
4 TraesCS3A01G096400 chr3D 48868337 48870658 2321 True 515.8 1024 94.4978 815 2519 5 chr3D.!!$R1 1704
5 TraesCS3A01G096400 chr2D 1623177 1624492 1315 True 830.0 830 78.6950 240 1525 1 chr2D.!!$R1 1285
6 TraesCS3A01G096400 chr2D 1621212 1622220 1008 False 627.0 627 78.3710 319 1325 1 chr2D.!!$F1 1006
7 TraesCS3A01G096400 chr2D 1817439 1818162 723 True 542.0 542 80.3550 605 1330 1 chr2D.!!$R2 725
8 TraesCS3A01G096400 chr2B 10215138 10216059 921 False 651.0 651 79.6650 577 1522 1 chr2B.!!$F1 945
9 TraesCS3A01G096400 chr4D 141360479 141361310 831 True 453.0 601 91.5195 1551 2173 2 chr4D.!!$R1 622
10 TraesCS3A01G096400 chr2A 708027 708733 706 False 534.0 534 80.5050 622 1327 1 chr2A.!!$F2 705
11 TraesCS3A01G096400 chr2A 702456 703162 706 False 529.0 529 80.3650 622 1327 1 chr2A.!!$F1 705

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
66 67 0.110678 TCTCACGTGAGACCTGGTCT 59.889 55.000 37.87 28.7 45.48 3.85 F
236 263 1.134491 TGCTGAGTAGATCGTCGGAGA 60.134 52.381 5.95 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1440 0.031857 TGTCTTTGTTGGCGCCATTG 59.968 50.0 33.25 17.98 0.00 2.82 R
1707 1913 0.674581 TGGTCAGCGGCAAATCTGAG 60.675 55.0 1.45 0.00 39.71 3.35 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 4.614555 TGATTTATGAATGCCACGTGTC 57.385 40.909 15.65 0.98 0.00 3.67
22 23 4.006319 TGATTTATGAATGCCACGTGTCA 58.994 39.130 15.65 8.63 0.00 3.58
23 24 4.639755 TGATTTATGAATGCCACGTGTCAT 59.360 37.500 19.43 19.43 35.05 3.06
24 25 4.614555 TTTATGAATGCCACGTGTCATC 57.385 40.909 19.16 11.02 32.99 2.92
25 26 2.408271 ATGAATGCCACGTGTCATCT 57.592 45.000 13.12 3.38 0.00 2.90
26 27 3.541996 ATGAATGCCACGTGTCATCTA 57.458 42.857 13.12 5.41 0.00 1.98
27 28 3.541996 TGAATGCCACGTGTCATCTAT 57.458 42.857 13.12 0.00 0.00 1.98
28 29 3.457234 TGAATGCCACGTGTCATCTATC 58.543 45.455 13.12 7.62 0.00 2.08
29 30 3.118811 TGAATGCCACGTGTCATCTATCA 60.119 43.478 13.12 10.21 0.00 2.15
30 31 2.584492 TGCCACGTGTCATCTATCAG 57.416 50.000 15.65 0.00 0.00 2.90
31 32 1.136891 TGCCACGTGTCATCTATCAGG 59.863 52.381 15.65 0.00 0.00 3.86
32 33 1.409064 GCCACGTGTCATCTATCAGGA 59.591 52.381 15.65 0.00 0.00 3.86
33 34 2.036475 GCCACGTGTCATCTATCAGGAT 59.964 50.000 15.65 0.00 0.00 3.24
34 35 3.858877 GCCACGTGTCATCTATCAGGATC 60.859 52.174 15.65 0.00 0.00 3.36
35 36 3.571828 CCACGTGTCATCTATCAGGATCT 59.428 47.826 15.65 0.00 0.00 2.75
36 37 4.762251 CCACGTGTCATCTATCAGGATCTA 59.238 45.833 15.65 0.00 0.00 1.98
37 38 5.417266 CCACGTGTCATCTATCAGGATCTAT 59.583 44.000 15.65 0.00 0.00 1.98
38 39 6.404184 CCACGTGTCATCTATCAGGATCTATC 60.404 46.154 15.65 0.00 0.00 2.08
39 40 6.150140 CACGTGTCATCTATCAGGATCTATCA 59.850 42.308 7.58 0.00 0.00 2.15
40 41 6.374053 ACGTGTCATCTATCAGGATCTATCAG 59.626 42.308 0.00 0.00 0.00 2.90
41 42 6.183360 CGTGTCATCTATCAGGATCTATCAGG 60.183 46.154 0.00 0.00 0.00 3.86
42 43 6.889177 GTGTCATCTATCAGGATCTATCAGGA 59.111 42.308 0.00 0.00 0.00 3.86
43 44 7.560991 GTGTCATCTATCAGGATCTATCAGGAT 59.439 40.741 0.00 0.00 0.00 3.24
44 45 7.560626 TGTCATCTATCAGGATCTATCAGGATG 59.439 40.741 0.00 0.00 37.54 3.51
45 46 7.014518 GTCATCTATCAGGATCTATCAGGATGG 59.985 44.444 0.00 4.12 36.16 3.51
46 47 5.775268 TCTATCAGGATCTATCAGGATGGG 58.225 45.833 0.00 1.62 36.16 4.00
47 48 3.931241 TCAGGATCTATCAGGATGGGT 57.069 47.619 0.00 0.00 36.16 4.51
48 49 3.784178 TCAGGATCTATCAGGATGGGTC 58.216 50.000 0.00 0.00 36.16 4.46
49 50 3.404081 TCAGGATCTATCAGGATGGGTCT 59.596 47.826 5.97 0.00 36.16 3.85
50 51 3.768757 CAGGATCTATCAGGATGGGTCTC 59.231 52.174 5.97 0.00 36.16 3.36
51 52 3.404081 AGGATCTATCAGGATGGGTCTCA 59.596 47.826 5.97 0.00 36.16 3.27
52 53 3.513515 GGATCTATCAGGATGGGTCTCAC 59.486 52.174 5.97 0.00 36.16 3.51
53 54 2.587522 TCTATCAGGATGGGTCTCACG 58.412 52.381 0.00 0.00 36.16 4.35
54 55 2.091830 TCTATCAGGATGGGTCTCACGT 60.092 50.000 0.00 0.00 36.16 4.49
55 56 0.826715 ATCAGGATGGGTCTCACGTG 59.173 55.000 9.94 9.94 36.16 4.49
56 57 0.251608 TCAGGATGGGTCTCACGTGA 60.252 55.000 18.88 18.88 36.16 4.35
57 58 0.174389 CAGGATGGGTCTCACGTGAG 59.826 60.000 34.76 34.76 43.36 3.51
58 59 4.542236 TCAGGATGGGTCTCACGTGAGA 62.542 54.545 37.87 37.87 42.39 3.27
64 65 4.923068 TCTCACGTGAGACCTGGT 57.077 55.556 37.87 0.00 45.48 4.00
65 66 2.642425 TCTCACGTGAGACCTGGTC 58.358 57.895 37.87 19.20 45.48 4.02
66 67 0.110678 TCTCACGTGAGACCTGGTCT 59.889 55.000 37.87 28.70 45.48 3.85
79 80 6.882768 AGACCTGGTCTCATAGAATTCTTT 57.117 37.500 23.49 2.41 38.71 2.52
80 81 7.264294 AGACCTGGTCTCATAGAATTCTTTT 57.736 36.000 23.49 0.00 38.71 2.27
81 82 7.334858 AGACCTGGTCTCATAGAATTCTTTTC 58.665 38.462 23.49 0.00 38.71 2.29
82 83 6.418946 ACCTGGTCTCATAGAATTCTTTTCC 58.581 40.000 14.36 8.65 0.00 3.13
83 84 6.216456 ACCTGGTCTCATAGAATTCTTTTCCT 59.784 38.462 14.36 0.00 0.00 3.36
84 85 6.765512 CCTGGTCTCATAGAATTCTTTTCCTC 59.234 42.308 14.36 1.53 0.00 3.71
85 86 6.341316 TGGTCTCATAGAATTCTTTTCCTCG 58.659 40.000 14.36 0.00 0.00 4.63
86 87 6.154534 TGGTCTCATAGAATTCTTTTCCTCGA 59.845 38.462 14.36 0.00 0.00 4.04
87 88 6.699642 GGTCTCATAGAATTCTTTTCCTCGAG 59.300 42.308 14.36 5.13 0.00 4.04
88 89 7.416890 GGTCTCATAGAATTCTTTTCCTCGAGA 60.417 40.741 15.71 10.37 0.00 4.04
89 90 7.434013 GTCTCATAGAATTCTTTTCCTCGAGAC 59.566 40.741 15.71 17.19 38.14 3.36
90 91 7.340743 TCTCATAGAATTCTTTTCCTCGAGACT 59.659 37.037 15.71 0.39 0.00 3.24
91 92 8.521170 TCATAGAATTCTTTTCCTCGAGACTA 57.479 34.615 15.71 0.00 0.00 2.59
92 93 8.625651 TCATAGAATTCTTTTCCTCGAGACTAG 58.374 37.037 15.71 5.78 0.00 2.57
93 94 8.625651 CATAGAATTCTTTTCCTCGAGACTAGA 58.374 37.037 15.71 8.10 0.00 2.43
97 98 4.011023 TCTTTTCCTCGAGACTAGACCTG 58.989 47.826 15.71 0.00 0.00 4.00
128 129 1.811266 CGCCGTGGTTCTGATCCAG 60.811 63.158 7.70 0.00 35.49 3.86
132 133 1.442769 CGTGGTTCTGATCCAGGTTG 58.557 55.000 15.83 2.06 36.48 3.77
217 236 1.525923 CCAGGAGAGCAGGGTCATG 59.474 63.158 0.97 0.00 0.00 3.07
231 258 2.287909 GGGTCATGCTGAGTAGATCGTC 60.288 54.545 0.00 0.00 0.00 4.20
232 259 2.603412 GGTCATGCTGAGTAGATCGTCG 60.603 54.545 0.00 0.00 0.00 5.12
233 260 1.604278 TCATGCTGAGTAGATCGTCGG 59.396 52.381 0.00 0.00 0.00 4.79
234 261 1.604278 CATGCTGAGTAGATCGTCGGA 59.396 52.381 5.95 0.00 0.00 4.55
235 262 1.300481 TGCTGAGTAGATCGTCGGAG 58.700 55.000 5.95 0.00 0.00 4.63
236 263 1.134491 TGCTGAGTAGATCGTCGGAGA 60.134 52.381 5.95 0.00 0.00 3.71
237 264 1.529438 GCTGAGTAGATCGTCGGAGAG 59.471 57.143 5.95 0.00 36.95 3.20
238 265 2.828877 CTGAGTAGATCGTCGGAGAGT 58.171 52.381 0.00 0.00 36.95 3.24
495 537 1.609072 GTCTCCAAAAAGCCAGGTGAC 59.391 52.381 0.00 0.00 38.33 3.67
544 586 1.600957 CTGCCGACCAATCATGTCATC 59.399 52.381 0.00 0.00 32.91 2.92
831 910 3.005539 AGGTCCTGGCACTGCGAT 61.006 61.111 0.00 0.00 0.00 4.58
860 939 4.626081 GCCCCCGTGGATCATCCG 62.626 72.222 0.00 0.00 40.17 4.18
884 963 1.812686 AAGCACGCCTTGGTCTACGA 61.813 55.000 0.00 0.00 33.68 3.43
885 964 1.805945 GCACGCCTTGGTCTACGAG 60.806 63.158 0.00 0.00 0.00 4.18
1177 1262 1.648467 GGAGTGGCAGCCGAATGAAC 61.648 60.000 7.03 0.00 0.00 3.18
1219 1304 3.672295 CTCGGCTCAGGCAGGTTCC 62.672 68.421 0.00 0.00 40.87 3.62
1234 1321 2.155279 GGTTCCTCTTTGCTGACTTCC 58.845 52.381 0.00 0.00 0.00 3.46
1238 1325 4.543590 TCCTCTTTGCTGACTTCCTTAG 57.456 45.455 0.00 0.00 0.00 2.18
1269 1356 2.375766 CGACAAGGACAGCAGCGAC 61.376 63.158 0.00 0.00 0.00 5.19
1276 1363 1.499056 GACAGCAGCGACATGGTTG 59.501 57.895 0.00 0.00 0.00 3.77
1337 1433 1.253593 TACGGCAATGGCAATGGCAA 61.254 50.000 26.02 12.57 42.43 4.52
1338 1434 1.812093 CGGCAATGGCAATGGCAAG 60.812 57.895 26.02 10.79 42.43 4.01
1340 1436 1.450669 GCAATGGCAATGGCAAGGG 60.451 57.895 14.81 7.44 42.43 3.95
1341 1437 1.450669 CAATGGCAATGGCAAGGGC 60.451 57.895 14.81 8.13 42.43 5.19
1342 1438 3.021473 AATGGCAATGGCAAGGGCG 62.021 57.895 14.81 0.00 42.43 6.13
1346 1442 3.693471 CAATGGCAAGGGCGGCAA 61.693 61.111 12.47 0.00 45.48 4.52
1347 1443 2.684655 AATGGCAAGGGCGGCAAT 60.685 55.556 12.47 0.00 45.48 3.56
1348 1444 3.021473 AATGGCAAGGGCGGCAATG 62.021 57.895 12.47 10.20 45.48 2.82
1446 1560 0.740737 GCAAAGGGATGATTCGTGGG 59.259 55.000 0.00 0.00 0.00 4.61
1476 1590 2.766970 TTAAGCACAAGTCCAAACGC 57.233 45.000 0.00 0.00 0.00 4.84
1525 1639 1.486310 AGGCGGTGCTCTGAATGATTA 59.514 47.619 0.00 0.00 0.00 1.75
1528 1642 2.289002 GCGGTGCTCTGAATGATTAAGG 59.711 50.000 0.00 0.00 0.00 2.69
1530 1644 3.806521 CGGTGCTCTGAATGATTAAGGAG 59.193 47.826 0.00 0.00 0.00 3.69
1531 1645 4.442052 CGGTGCTCTGAATGATTAAGGAGA 60.442 45.833 5.95 0.00 0.00 3.71
1556 1752 9.534565 GATATCAGTTCAGTTTACTATTGCTGA 57.465 33.333 0.00 0.00 36.35 4.26
1591 1787 3.997021 CTCCCTGTTTACAGCAAGTAGTG 59.003 47.826 4.34 0.00 42.47 2.74
1612 1813 5.302059 AGTGCTGACTCTAGTGTTAAGTCAA 59.698 40.000 11.20 0.00 46.30 3.18
1734 1940 3.951775 TTGCCGCTGACCAAATAATTT 57.048 38.095 0.00 0.00 0.00 1.82
1798 2211 4.886579 AGCTGAGGTAATTTTGGCAAAAG 58.113 39.130 27.21 14.08 33.22 2.27
1803 2216 7.546778 TGAGGTAATTTTGGCAAAAGAAAAC 57.453 32.000 27.21 20.46 33.22 2.43
1852 2265 3.700539 TGGTCATTTGCCAATATGACTGG 59.299 43.478 21.23 0.00 46.22 4.00
2010 2435 3.442977 GGCTTGAATGCTGAATGACTTCT 59.557 43.478 0.00 0.00 32.29 2.85
2174 2602 0.386731 GATGGCCAACAAACGAACGG 60.387 55.000 10.96 0.00 0.00 4.44
2177 2605 2.051703 CCAACAAACGAACGGCGG 60.052 61.111 13.24 0.00 46.49 6.13
2271 2702 7.350467 CAGCTGCTTGATATACAACTGTAATG 58.650 38.462 0.00 0.00 33.76 1.90
2292 2723 3.210857 GTGTCTAGACGCCAGCAAA 57.789 52.632 23.26 0.00 35.90 3.68
2303 2734 0.109597 GCCAGCAAACGTCTTCCATG 60.110 55.000 0.00 0.00 0.00 3.66
2354 2785 2.225017 TGGAAACATCTTCAACCCCTCC 60.225 50.000 0.00 0.00 33.40 4.30
2395 2826 5.307204 CCATTCCCTGCAAATTCAGAAAAA 58.693 37.500 0.00 0.00 36.19 1.94
2413 2844 6.980397 CAGAAAAACAAAACATAGAGCAGGTT 59.020 34.615 0.00 0.00 30.97 3.50
2465 3255 8.035394 CGTTTATGCATATAGGGATAACAGTCT 58.965 37.037 10.39 0.00 31.89 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.614555 TGACACGTGGCATTCATAAATC 57.385 40.909 23.03 3.54 0.00 2.17
2 3 4.883585 AGATGACACGTGGCATTCATAAAT 59.116 37.500 36.07 14.34 45.42 1.40
3 4 4.260985 AGATGACACGTGGCATTCATAAA 58.739 39.130 36.07 7.37 45.42 1.40
4 5 3.872696 AGATGACACGTGGCATTCATAA 58.127 40.909 36.07 8.22 45.42 1.90
5 6 3.541996 AGATGACACGTGGCATTCATA 57.458 42.857 36.07 9.07 45.42 2.15
6 7 2.408271 AGATGACACGTGGCATTCAT 57.592 45.000 36.07 25.62 45.42 2.57
7 8 3.118811 TGATAGATGACACGTGGCATTCA 60.119 43.478 36.07 30.53 45.42 2.57
8 9 3.457234 TGATAGATGACACGTGGCATTC 58.543 45.455 36.07 28.46 45.42 2.67
9 10 3.461061 CTGATAGATGACACGTGGCATT 58.539 45.455 36.07 26.04 45.42 3.56
11 12 1.136891 CCTGATAGATGACACGTGGCA 59.863 52.381 29.28 29.28 37.54 4.92
12 13 1.409064 TCCTGATAGATGACACGTGGC 59.591 52.381 21.57 19.24 0.00 5.01
13 14 3.571828 AGATCCTGATAGATGACACGTGG 59.428 47.826 21.57 1.66 0.00 4.94
14 15 4.844998 AGATCCTGATAGATGACACGTG 57.155 45.455 15.48 15.48 0.00 4.49
15 16 6.241645 TGATAGATCCTGATAGATGACACGT 58.758 40.000 0.00 0.00 0.00 4.49
16 17 6.183360 CCTGATAGATCCTGATAGATGACACG 60.183 46.154 0.00 0.00 0.00 4.49
17 18 6.889177 TCCTGATAGATCCTGATAGATGACAC 59.111 42.308 0.00 0.00 0.00 3.67
18 19 7.037342 TCCTGATAGATCCTGATAGATGACA 57.963 40.000 0.00 0.00 0.00 3.58
19 20 7.014518 CCATCCTGATAGATCCTGATAGATGAC 59.985 44.444 10.34 0.00 31.27 3.06
20 21 7.068061 CCATCCTGATAGATCCTGATAGATGA 58.932 42.308 10.34 0.00 31.27 2.92
21 22 6.268158 CCCATCCTGATAGATCCTGATAGATG 59.732 46.154 0.00 0.00 0.00 2.90
22 23 6.067721 ACCCATCCTGATAGATCCTGATAGAT 60.068 42.308 0.00 0.00 0.00 1.98
23 24 5.257339 ACCCATCCTGATAGATCCTGATAGA 59.743 44.000 0.00 0.00 0.00 1.98
24 25 5.527385 ACCCATCCTGATAGATCCTGATAG 58.473 45.833 0.00 0.00 0.00 2.08
25 26 5.257339 AGACCCATCCTGATAGATCCTGATA 59.743 44.000 0.00 0.00 0.00 2.15
26 27 4.047006 AGACCCATCCTGATAGATCCTGAT 59.953 45.833 0.00 0.00 0.00 2.90
27 28 3.404081 AGACCCATCCTGATAGATCCTGA 59.596 47.826 0.00 0.00 0.00 3.86
28 29 3.768757 GAGACCCATCCTGATAGATCCTG 59.231 52.174 0.00 0.00 0.00 3.86
29 30 3.404081 TGAGACCCATCCTGATAGATCCT 59.596 47.826 0.00 0.00 0.00 3.24
30 31 3.513515 GTGAGACCCATCCTGATAGATCC 59.486 52.174 0.00 0.00 0.00 3.36
31 32 3.192422 CGTGAGACCCATCCTGATAGATC 59.808 52.174 0.00 0.00 0.00 2.75
32 33 3.161067 CGTGAGACCCATCCTGATAGAT 58.839 50.000 0.00 0.00 0.00 1.98
33 34 2.091830 ACGTGAGACCCATCCTGATAGA 60.092 50.000 0.00 0.00 0.00 1.98
34 35 2.035193 CACGTGAGACCCATCCTGATAG 59.965 54.545 10.90 0.00 0.00 2.08
35 36 2.031870 CACGTGAGACCCATCCTGATA 58.968 52.381 10.90 0.00 0.00 2.15
36 37 0.826715 CACGTGAGACCCATCCTGAT 59.173 55.000 10.90 0.00 0.00 2.90
37 38 0.251608 TCACGTGAGACCCATCCTGA 60.252 55.000 15.76 0.00 0.00 3.86
38 39 0.174389 CTCACGTGAGACCCATCCTG 59.826 60.000 36.73 9.65 44.74 3.86
39 40 0.039764 TCTCACGTGAGACCCATCCT 59.960 55.000 37.87 0.00 45.48 3.24
40 41 2.579878 TCTCACGTGAGACCCATCC 58.420 57.895 37.87 0.00 45.48 3.51
48 49 2.647356 AGACCAGGTCTCACGTGAG 58.353 57.895 34.76 34.76 38.71 3.51
49 50 4.923068 AGACCAGGTCTCACGTGA 57.077 55.556 17.31 18.88 38.71 4.35
56 57 6.882768 AAAGAATTCTATGAGACCAGGTCT 57.117 37.500 23.18 23.18 46.42 3.85
57 58 6.540551 GGAAAAGAATTCTATGAGACCAGGTC 59.459 42.308 12.25 12.25 0.00 3.85
58 59 6.216456 AGGAAAAGAATTCTATGAGACCAGGT 59.784 38.462 8.75 0.00 0.00 4.00
59 60 6.657875 AGGAAAAGAATTCTATGAGACCAGG 58.342 40.000 8.75 0.00 0.00 4.45
60 61 6.478344 CGAGGAAAAGAATTCTATGAGACCAG 59.522 42.308 8.75 2.85 0.00 4.00
61 62 6.154534 TCGAGGAAAAGAATTCTATGAGACCA 59.845 38.462 8.75 0.00 0.00 4.02
62 63 6.574350 TCGAGGAAAAGAATTCTATGAGACC 58.426 40.000 8.75 7.08 0.00 3.85
63 64 7.434013 GTCTCGAGGAAAAGAATTCTATGAGAC 59.566 40.741 13.56 20.32 40.17 3.36
64 65 7.340743 AGTCTCGAGGAAAAGAATTCTATGAGA 59.659 37.037 13.56 10.32 0.00 3.27
65 66 7.488322 AGTCTCGAGGAAAAGAATTCTATGAG 58.512 38.462 13.56 8.37 0.00 2.90
66 67 7.411486 AGTCTCGAGGAAAAGAATTCTATGA 57.589 36.000 13.56 0.00 0.00 2.15
67 68 8.625651 TCTAGTCTCGAGGAAAAGAATTCTATG 58.374 37.037 13.56 0.00 0.00 2.23
68 69 8.626526 GTCTAGTCTCGAGGAAAAGAATTCTAT 58.373 37.037 13.56 0.41 0.00 1.98
69 70 7.067251 GGTCTAGTCTCGAGGAAAAGAATTCTA 59.933 40.741 13.56 0.00 0.00 2.10
70 71 6.127563 GGTCTAGTCTCGAGGAAAAGAATTCT 60.128 42.308 13.56 0.88 0.00 2.40
71 72 6.037726 GGTCTAGTCTCGAGGAAAAGAATTC 58.962 44.000 13.56 0.00 0.00 2.17
72 73 5.717654 AGGTCTAGTCTCGAGGAAAAGAATT 59.282 40.000 13.56 0.78 0.00 2.17
73 74 5.126384 CAGGTCTAGTCTCGAGGAAAAGAAT 59.874 44.000 13.56 0.00 0.00 2.40
74 75 4.459685 CAGGTCTAGTCTCGAGGAAAAGAA 59.540 45.833 13.56 0.00 0.00 2.52
75 76 4.011023 CAGGTCTAGTCTCGAGGAAAAGA 58.989 47.826 13.56 7.97 0.00 2.52
76 77 3.428316 GCAGGTCTAGTCTCGAGGAAAAG 60.428 52.174 13.56 5.69 0.00 2.27
77 78 2.492484 GCAGGTCTAGTCTCGAGGAAAA 59.508 50.000 13.56 0.00 0.00 2.29
78 79 2.093106 GCAGGTCTAGTCTCGAGGAAA 58.907 52.381 13.56 0.00 0.00 3.13
79 80 1.682394 GGCAGGTCTAGTCTCGAGGAA 60.682 57.143 13.56 0.00 0.00 3.36
80 81 0.107116 GGCAGGTCTAGTCTCGAGGA 60.107 60.000 13.56 0.00 0.00 3.71
81 82 0.106918 AGGCAGGTCTAGTCTCGAGG 60.107 60.000 13.56 0.00 0.00 4.63
82 83 1.305201 GAGGCAGGTCTAGTCTCGAG 58.695 60.000 5.93 5.93 0.00 4.04
83 84 0.107116 GGAGGCAGGTCTAGTCTCGA 60.107 60.000 0.00 0.00 0.00 4.04
84 85 0.106918 AGGAGGCAGGTCTAGTCTCG 60.107 60.000 0.00 0.00 0.00 4.04
85 86 1.687563 GAGGAGGCAGGTCTAGTCTC 58.312 60.000 0.00 0.00 0.00 3.36
86 87 0.260523 GGAGGAGGCAGGTCTAGTCT 59.739 60.000 0.00 0.00 0.00 3.24
87 88 0.757561 GGGAGGAGGCAGGTCTAGTC 60.758 65.000 0.00 0.00 0.00 2.59
88 89 1.225403 AGGGAGGAGGCAGGTCTAGT 61.225 60.000 0.00 0.00 0.00 2.57
89 90 0.469144 GAGGGAGGAGGCAGGTCTAG 60.469 65.000 0.00 0.00 0.00 2.43
90 91 1.621377 GAGGGAGGAGGCAGGTCTA 59.379 63.158 0.00 0.00 0.00 2.59
91 92 2.366570 GAGGGAGGAGGCAGGTCT 59.633 66.667 0.00 0.00 0.00 3.85
92 93 2.766229 GGAGGGAGGAGGCAGGTC 60.766 72.222 0.00 0.00 0.00 3.85
93 94 4.423209 GGGAGGGAGGAGGCAGGT 62.423 72.222 0.00 0.00 0.00 4.00
115 116 0.038166 GCCAACCTGGATCAGAACCA 59.962 55.000 0.00 0.00 40.96 3.67
116 117 0.681243 GGCCAACCTGGATCAGAACC 60.681 60.000 0.00 0.00 40.96 3.62
128 129 4.171103 ATCTACCGGCGGCCAACC 62.171 66.667 28.71 1.78 0.00 3.77
132 133 3.537874 ACAGATCTACCGGCGGCC 61.538 66.667 28.71 9.54 0.00 6.13
217 236 1.529438 CTCTCCGACGATCTACTCAGC 59.471 57.143 0.00 0.00 0.00 4.26
231 258 1.652012 GCTCATCTCCGACTCTCCG 59.348 63.158 0.00 0.00 0.00 4.63
232 259 1.652012 CGCTCATCTCCGACTCTCC 59.348 63.158 0.00 0.00 0.00 3.71
233 260 1.652012 CCGCTCATCTCCGACTCTC 59.348 63.158 0.00 0.00 0.00 3.20
234 261 2.485795 GCCGCTCATCTCCGACTCT 61.486 63.158 0.00 0.00 0.00 3.24
235 262 2.026879 GCCGCTCATCTCCGACTC 59.973 66.667 0.00 0.00 0.00 3.36
236 263 3.893763 CGCCGCTCATCTCCGACT 61.894 66.667 0.00 0.00 0.00 4.18
237 264 4.933064 CCGCCGCTCATCTCCGAC 62.933 72.222 0.00 0.00 0.00 4.79
495 537 4.609018 CTACCGGCGGCCTCATGG 62.609 72.222 28.71 13.18 0.00 3.66
544 586 2.406616 CGCGGTGGGGAAGAAATGG 61.407 63.158 0.00 0.00 0.00 3.16
616 685 1.588082 GTGGAGGTTTGGCATGCTG 59.412 57.895 18.92 0.00 0.00 4.41
860 939 4.347453 CCAAGGCGTGCTTGTGGC 62.347 66.667 0.00 0.00 42.22 5.01
987 1066 2.969238 GGCATGATCCAGTCGCCG 60.969 66.667 0.00 0.00 32.14 6.46
1177 1262 2.200067 GATGATCTTGGAGTCGCACAG 58.800 52.381 0.00 0.00 0.00 3.66
1219 1304 4.688413 GTCACTAAGGAAGTCAGCAAAGAG 59.312 45.833 0.00 0.00 35.76 2.85
1234 1321 6.368791 TCCTTGTCGAATTTCATGTCACTAAG 59.631 38.462 0.00 0.00 0.00 2.18
1238 1325 4.213270 TGTCCTTGTCGAATTTCATGTCAC 59.787 41.667 0.00 0.00 0.00 3.67
1343 1439 1.006337 TCTTTGTTGGCGCCATTGC 60.006 52.632 33.25 23.06 0.00 3.56
1344 1440 0.031857 TGTCTTTGTTGGCGCCATTG 59.968 50.000 33.25 17.98 0.00 2.82
1345 1441 0.749649 TTGTCTTTGTTGGCGCCATT 59.250 45.000 33.25 0.00 0.00 3.16
1346 1442 0.968405 ATTGTCTTTGTTGGCGCCAT 59.032 45.000 33.25 8.24 0.00 4.40
1347 1443 0.749649 AATTGTCTTTGTTGGCGCCA 59.250 45.000 29.03 29.03 0.00 5.69
1348 1444 1.792367 GAAATTGTCTTTGTTGGCGCC 59.208 47.619 22.73 22.73 0.00 6.53
1349 1445 2.468831 TGAAATTGTCTTTGTTGGCGC 58.531 42.857 0.00 0.00 0.00 6.53
1350 1446 4.026640 CAGTTGAAATTGTCTTTGTTGGCG 60.027 41.667 0.00 0.00 0.00 5.69
1446 1560 5.470845 ACTTGTGCTTAATCATACGAAGC 57.529 39.130 0.00 0.00 44.71 3.86
1476 1590 5.447010 GCTCAGCTGCTTCTTAAACATGTAG 60.447 44.000 9.47 0.00 0.00 2.74
1528 1642 9.757227 AGCAATAGTAAACTGAACTGATATCTC 57.243 33.333 3.98 0.00 0.00 2.75
1530 1644 9.534565 TCAGCAATAGTAAACTGAACTGATATC 57.465 33.333 0.00 0.00 36.27 1.63
1549 1745 4.082354 GGAGCAGAAACAAAGATCAGCAAT 60.082 41.667 0.00 0.00 31.25 3.56
1556 1752 3.515602 ACAGGGAGCAGAAACAAAGAT 57.484 42.857 0.00 0.00 0.00 2.40
1625 1826 2.579207 CCACAGGATGGTACTGTACG 57.421 55.000 11.52 0.00 46.76 3.67
1707 1913 0.674581 TGGTCAGCGGCAAATCTGAG 60.675 55.000 1.45 0.00 39.71 3.35
1734 1940 3.380004 AGTTCGAAAACTGCCATCAAACA 59.620 39.130 0.00 0.00 44.13 2.83
1782 1988 8.972262 TTTTGTTTTCTTTTGCCAAAATTACC 57.028 26.923 2.58 0.00 31.97 2.85
1798 2211 4.202253 ACTCCAGCTCCCAATTTTGTTTTC 60.202 41.667 0.00 0.00 0.00 2.29
1803 2216 3.944015 CTCTACTCCAGCTCCCAATTTTG 59.056 47.826 0.00 0.00 0.00 2.44
1852 2265 6.129179 TCTCCAAAATTCCTGAATATCCCAC 58.871 40.000 0.00 0.00 0.00 4.61
1959 2384 5.130311 ACCAAACTGCTGTAATTCCCTTTTT 59.870 36.000 0.00 0.00 0.00 1.94
2029 2454 9.967451 TGATCATGTGTCCTATTTAAACCTAAA 57.033 29.630 0.00 0.00 0.00 1.85
2102 2528 7.453141 AAATTAGAAGGCCTCTAACATAGGT 57.547 36.000 20.25 7.05 46.96 3.08
2177 2605 1.300963 TCCATGGCTGGAGCTGTTC 59.699 57.895 6.96 0.00 46.95 3.18
2271 2702 1.139947 GCTGGCGTCTAGACACCTC 59.860 63.158 26.23 16.15 34.71 3.85
2292 2723 3.006967 AGCTTGTACTTCATGGAAGACGT 59.993 43.478 12.56 0.00 41.71 4.34
2303 2734 8.541133 ACTTAAAGATGAAGAGCTTGTACTTC 57.459 34.615 6.05 6.05 41.67 3.01
2415 2846 8.204160 ACGAGAATGTAGTTGATCAATAATCCA 58.796 33.333 12.12 5.22 33.01 3.41
2465 3255 5.246203 AGTGATTACAGAAAGGCAGACTGTA 59.754 40.000 3.99 11.51 43.27 2.74
2466 3256 4.040952 AGTGATTACAGAAAGGCAGACTGT 59.959 41.667 3.99 13.07 45.06 3.55
2467 3257 4.573900 AGTGATTACAGAAAGGCAGACTG 58.426 43.478 0.00 0.00 37.62 3.51


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

AutoCloner maintained by Alex Coulton.