Multiple sequence alignment - TraesCS1B01G162900

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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 TraesCS1B01G162900 chr1B 100.000 2321 0 0 1 2321 282428891 282431211 0.000000e+00 4287.0
1 TraesCS1B01G162900 chr1B 82.282 412 64 9 1727 2135 489997591 489997996 4.750000e-92 348.0
2 TraesCS1B01G162900 chr1B 78.268 589 88 22 848 1423 338039970 338040531 2.210000e-90 342.0
3 TraesCS1B01G162900 chr1B 87.143 210 23 4 2113 2321 489997795 489998001 3.860000e-58 235.0
4 TraesCS1B01G162900 chr1B 84.615 182 28 0 367 548 276012108 276011927 5.090000e-42 182.0
5 TraesCS1B01G162900 chr3B 84.084 999 112 24 546 1527 192362509 192361541 0.000000e+00 920.0
6 TraesCS1B01G162900 chr3B 86.550 513 56 12 1605 2114 761041198 761040696 9.370000e-154 553.0
7 TraesCS1B01G162900 chr3B 79.610 770 108 35 1536 2293 776502801 776502069 7.400000e-140 507.0
8 TraesCS1B01G162900 chr3B 84.884 344 36 15 1984 2321 109795000 109794667 1.330000e-87 333.0
9 TraesCS1B01G162900 chr3B 89.243 251 21 5 116 363 506301069 506300822 2.240000e-80 309.0
10 TraesCS1B01G162900 chr3B 82.890 263 32 12 2064 2321 761040963 761040709 8.350000e-55 224.0
11 TraesCS1B01G162900 chr3D 86.530 876 67 29 666 1533 439093269 439092437 0.000000e+00 917.0
12 TraesCS1B01G162900 chr3D 90.113 617 44 7 63 667 439093937 439093326 0.000000e+00 785.0
13 TraesCS1B01G162900 chr3D 89.879 247 21 4 116 359 465771032 465771277 4.810000e-82 315.0
14 TraesCS1B01G162900 chr3D 80.822 365 57 12 1965 2321 261000560 261000919 8.170000e-70 274.0
15 TraesCS1B01G162900 chr3D 81.212 165 25 5 600 763 204183302 204183143 6.730000e-26 128.0
16 TraesCS1B01G162900 chr3D 96.552 58 1 1 1 58 439072295 439072239 6.830000e-16 95.3
17 TraesCS1B01G162900 chr3D 92.188 64 5 0 1 64 439094241 439094178 8.830000e-15 91.6
18 TraesCS1B01G162900 chr5D 83.800 1000 119 24 546 1527 253800828 253799854 0.000000e+00 909.0
19 TraesCS1B01G162900 chr5D 90.761 184 13 3 367 548 253801276 253801095 2.300000e-60 243.0
20 TraesCS1B01G162900 chr5D 80.851 282 33 14 597 861 80799291 80799568 3.910000e-48 202.0
21 TraesCS1B01G162900 chr4B 87.836 781 59 11 1536 2293 392736945 392736178 0.000000e+00 883.0
22 TraesCS1B01G162900 chr4B 79.970 664 86 26 1536 2172 424751742 424752385 1.640000e-121 446.0
23 TraesCS1B01G162900 chr4B 87.887 355 37 6 1969 2321 392736577 392736227 1.660000e-111 412.0
24 TraesCS1B01G162900 chr6D 84.282 808 94 20 734 1526 258784200 258784989 0.000000e+00 758.0
25 TraesCS1B01G162900 chr6D 78.297 599 111 15 850 1432 106838145 106838740 3.640000e-98 368.0
26 TraesCS1B01G162900 chr6D 89.641 251 20 5 116 363 173194371 173194618 4.810000e-82 315.0
27 TraesCS1B01G162900 chr6D 89.243 251 21 5 116 363 187434214 187434461 2.240000e-80 309.0
28 TraesCS1B01G162900 chr6D 89.069 247 21 5 116 359 169579617 169579860 3.750000e-78 302.0
29 TraesCS1B01G162900 chr6D 90.110 182 18 0 367 548 120842764 120842583 1.070000e-58 237.0
30 TraesCS1B01G162900 chr6D 89.840 187 15 3 364 548 258783447 258783631 1.070000e-58 237.0
31 TraesCS1B01G162900 chr6D 80.851 282 33 14 597 861 135216332 135216055 3.910000e-48 202.0
32 TraesCS1B01G162900 chr7B 89.456 607 46 18 1534 2135 666327374 666327967 0.000000e+00 750.0
33 TraesCS1B01G162900 chr7B 85.350 628 75 15 1536 2156 74858152 74858769 3.250000e-178 634.0
34 TraesCS1B01G162900 chr2B 84.076 628 84 15 1535 2156 157684076 157683459 1.990000e-165 592.0
35 TraesCS1B01G162900 chr2B 88.800 250 24 4 116 362 406032060 406031812 1.040000e-78 303.0
36 TraesCS1B01G162900 chr2B 80.000 85 8 8 767 846 434013564 434013644 1.000000e-03 54.7
37 TraesCS1B01G162900 chr6A 82.009 667 79 15 546 1209 234623384 234622756 1.580000e-146 529.0
38 TraesCS1B01G162900 chr6A 82.353 323 43 7 1206 1526 234616330 234616020 3.800000e-68 268.0
39 TraesCS1B01G162900 chr6A 90.110 182 18 0 367 548 158474170 158474351 1.070000e-58 237.0
40 TraesCS1B01G162900 chr1A 84.337 498 70 7 1034 1526 194524242 194523748 4.490000e-132 481.0
41 TraesCS1B01G162900 chr1A 81.562 461 46 20 546 1004 194524661 194524238 6.140000e-91 344.0
42 TraesCS1B01G162900 chr1A 88.587 184 17 3 367 548 194525103 194524922 1.080000e-53 220.0
43 TraesCS1B01G162900 chr4A 79.753 647 84 23 1536 2156 649003355 649002730 2.130000e-115 425.0
44 TraesCS1B01G162900 chr4A 85.876 177 25 0 366 542 213397176 213397352 3.040000e-44 189.0
45 TraesCS1B01G162900 chr6B 79.528 635 94 22 1535 2152 452742197 452742812 9.920000e-114 420.0
46 TraesCS1B01G162900 chr6B 90.417 240 20 2 125 362 196918438 196918200 1.730000e-81 313.0
47 TraesCS1B01G162900 chr6B 90.110 182 18 0 367 548 212171825 212172006 1.070000e-58 237.0
48 TraesCS1B01G162900 chr6B 77.458 417 50 31 1889 2293 157674952 157675336 2.340000e-50 209.0
49 TraesCS1B01G162900 chr6B 82.143 168 23 5 597 763 245429535 245429374 1.120000e-28 137.0
50 TraesCS1B01G162900 chr7D 78.488 516 88 17 848 1352 298814603 298814100 1.340000e-82 316.0
51 TraesCS1B01G162900 chr7D 80.226 177 26 7 597 770 431617659 431617489 8.710000e-25 124.0
52 TraesCS1B01G162900 chr3A 77.985 536 91 16 902 1423 499239983 499240505 6.230000e-81 311.0
53 TraesCS1B01G162900 chr3A 77.703 148 20 10 1890 2029 575753146 575753288 6.880000e-11 78.7
54 TraesCS1B01G162900 chr2A 87.984 258 25 4 107 362 506720890 506720637 1.350000e-77 300.0
55 TraesCS1B01G162900 chr2A 78.676 408 70 16 1921 2321 707166244 707165847 2.960000e-64 255.0
56 TraesCS1B01G162900 chr4D 77.458 417 71 23 1890 2297 477406686 477407088 6.450000e-56 228.0
57 TraesCS1B01G162900 chr1D 80.412 97 17 2 761 855 103683675 103683771 3.200000e-09 73.1


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 TraesCS1B01G162900 chr1B 282428891 282431211 2320 False 4287.000000 4287 100.000000 1 2321 1 chr1B.!!$F1 2320
1 TraesCS1B01G162900 chr1B 338039970 338040531 561 False 342.000000 342 78.268000 848 1423 1 chr1B.!!$F2 575
2 TraesCS1B01G162900 chr3B 192361541 192362509 968 True 920.000000 920 84.084000 546 1527 1 chr3B.!!$R2 981
3 TraesCS1B01G162900 chr3B 776502069 776502801 732 True 507.000000 507 79.610000 1536 2293 1 chr3B.!!$R4 757
4 TraesCS1B01G162900 chr3B 761040696 761041198 502 True 388.500000 553 84.720000 1605 2321 2 chr3B.!!$R5 716
5 TraesCS1B01G162900 chr3D 439092437 439094241 1804 True 597.866667 917 89.610333 1 1533 3 chr3D.!!$R3 1532
6 TraesCS1B01G162900 chr5D 253799854 253801276 1422 True 576.000000 909 87.280500 367 1527 2 chr5D.!!$R1 1160
7 TraesCS1B01G162900 chr4B 392736178 392736945 767 True 647.500000 883 87.861500 1536 2321 2 chr4B.!!$R1 785
8 TraesCS1B01G162900 chr4B 424751742 424752385 643 False 446.000000 446 79.970000 1536 2172 1 chr4B.!!$F1 636
9 TraesCS1B01G162900 chr6D 258783447 258784989 1542 False 497.500000 758 87.061000 364 1526 2 chr6D.!!$F5 1162
10 TraesCS1B01G162900 chr6D 106838145 106838740 595 False 368.000000 368 78.297000 850 1432 1 chr6D.!!$F1 582
11 TraesCS1B01G162900 chr7B 666327374 666327967 593 False 750.000000 750 89.456000 1534 2135 1 chr7B.!!$F2 601
12 TraesCS1B01G162900 chr7B 74858152 74858769 617 False 634.000000 634 85.350000 1536 2156 1 chr7B.!!$F1 620
13 TraesCS1B01G162900 chr2B 157683459 157684076 617 True 592.000000 592 84.076000 1535 2156 1 chr2B.!!$R1 621
14 TraesCS1B01G162900 chr6A 234622756 234623384 628 True 529.000000 529 82.009000 546 1209 1 chr6A.!!$R2 663
15 TraesCS1B01G162900 chr1A 194523748 194525103 1355 True 348.333333 481 84.828667 367 1526 3 chr1A.!!$R1 1159
16 TraesCS1B01G162900 chr4A 649002730 649003355 625 True 425.000000 425 79.753000 1536 2156 1 chr4A.!!$R1 620
17 TraesCS1B01G162900 chr6B 452742197 452742812 615 False 420.000000 420 79.528000 1535 2152 1 chr6B.!!$F3 617
18 TraesCS1B01G162900 chr7D 298814100 298814603 503 True 316.000000 316 78.488000 848 1352 1 chr7D.!!$R1 504
19 TraesCS1B01G162900 chr3A 499239983 499240505 522 False 311.000000 311 77.985000 902 1423 1 chr3A.!!$F1 521

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
203 446 0.108186 TCTCTGTGTAGGGCAATGCG 60.108 55.000 0.0 0.0 0.0 4.73 F
1089 1854 1.204704 AGACACGATGCGATGGAAGAA 59.795 47.619 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1217 1985 0.392729 CCCAAGGAGAAGCTGCTCAG 60.393 60.000 23.57 11.96 36.62 3.35 R
1992 2840 7.093992 TCGAATTTCCAAAAAGTTCAACAACT 58.906 30.769 0.00 0.00 45.43 3.16 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
64 65 7.714813 TCTTTGTTGTCACATAATCACTTGAGA 59.285 33.333 0.00 0.00 31.06 3.27
75 151 1.760613 TCACTTGAGACTTTGGGACGT 59.239 47.619 0.00 0.00 0.00 4.34
165 408 4.574828 TGTCTCTTCAGTTTTCCTTTTCCG 59.425 41.667 0.00 0.00 0.00 4.30
177 420 4.823790 TCCTTTTCCGAAGTTTGCTAAC 57.176 40.909 2.56 2.56 34.36 2.34
189 432 6.237332 CGAAGTTTGCTAACGTATTCTCTCTG 60.237 42.308 5.38 0.00 39.31 3.35
203 446 0.108186 TCTCTGTGTAGGGCAATGCG 60.108 55.000 0.00 0.00 0.00 4.73
224 467 3.007290 CGATCCATGCTTCTATTGGGAGA 59.993 47.826 0.00 0.00 0.00 3.71
233 476 4.396478 GCTTCTATTGGGAGAAAACTGGTC 59.604 45.833 0.00 0.00 35.06 4.02
263 508 8.962884 AATTTAAAGCAAACATGAAAGGACTT 57.037 26.923 0.00 0.00 0.00 3.01
308 553 9.635520 CTTCAAAGTCTAGGAGTACGAAAAATA 57.364 33.333 0.00 0.00 0.00 1.40
310 555 8.579006 TCAAAGTCTAGGAGTACGAAAAATACA 58.421 33.333 0.00 0.00 0.00 2.29
319 564 6.592607 GGAGTACGAAAAATACAGACCATTGA 59.407 38.462 0.00 0.00 0.00 2.57
362 608 7.379529 CAGTTTTCTTTTTGATACAACAGCGAT 59.620 33.333 0.00 0.00 0.00 4.58
365 611 9.906660 TTTTCTTTTTGATACAACAGCGATTAT 57.093 25.926 0.00 0.00 0.00 1.28
397 643 2.915659 AAGACGTCGGTGGGCTGA 60.916 61.111 10.46 0.00 0.00 4.26
453 699 1.334869 CAGCTTGGCCGGATATTCAAC 59.665 52.381 5.05 0.00 0.00 3.18
485 731 2.492088 GGAAGTAGGCCAAACAACATCC 59.508 50.000 5.01 3.17 0.00 3.51
492 738 2.351738 GGCCAAACAACATCCGAAAGAG 60.352 50.000 0.00 0.00 0.00 2.85
567 1090 7.420563 GGGACATGATATGGCAGAATGGATATA 60.421 40.741 0.00 0.00 41.20 0.86
572 1095 9.794719 ATGATATGGCAGAATGGATATAATCTG 57.205 33.333 0.00 0.00 41.69 2.90
591 1114 6.909550 ATCTGCTACTCCTAGAAGTATTGG 57.090 41.667 0.00 0.00 31.55 3.16
655 1179 9.072375 TGAATAATACCAAATGTGACACTTTGA 57.928 29.630 21.82 10.69 34.93 2.69
670 1252 9.979270 GTGACACTTTGAGTTATCTGATATTTG 57.021 33.333 0.00 0.00 0.00 2.32
708 1293 2.751259 ACAAGCCAATAGTGACAGCATG 59.249 45.455 0.00 0.00 46.00 4.06
743 1458 9.056005 TCATTTTAGTTCATATGTAGGATGCAC 57.944 33.333 1.90 0.00 29.56 4.57
764 1479 7.190920 GCACTCGCAACTATTTTCCTATTAT 57.809 36.000 0.00 0.00 38.36 1.28
885 1614 7.399191 ACAGATATACACCTTCCACTAACAAGA 59.601 37.037 0.00 0.00 0.00 3.02
887 1616 8.993424 AGATATACACCTTCCACTAACAAGAAT 58.007 33.333 0.00 0.00 0.00 2.40
898 1628 9.457436 TTCCACTAACAAGAATTACCTTAATCC 57.543 33.333 0.00 0.00 0.00 3.01
921 1651 7.169591 TCCCATTATATTGGTTTACCCATACG 58.830 38.462 11.73 0.00 44.74 3.06
939 1669 5.446709 CATACGCATGCAGAAAAAGGATAG 58.553 41.667 19.57 0.00 0.00 2.08
980 1741 3.247162 AGAGGCAGGAAAAGAGAGAAGT 58.753 45.455 0.00 0.00 0.00 3.01
984 1747 2.877708 GCAGGAAAAGAGAGAAGTGGGG 60.878 54.545 0.00 0.00 0.00 4.96
1055 1818 2.493907 GAAGACGACCTGCCGAGCTT 62.494 60.000 0.00 0.00 33.35 3.74
1059 1822 2.415608 CGACCTGCCGAGCTTCCTA 61.416 63.158 0.00 0.00 0.00 2.94
1089 1854 1.204704 AGACACGATGCGATGGAAGAA 59.795 47.619 0.00 0.00 0.00 2.52
1091 1856 2.609459 GACACGATGCGATGGAAGAAAT 59.391 45.455 0.00 0.00 0.00 2.17
1107 1874 2.437281 AGAAATCCGTCAGCATCCTCAT 59.563 45.455 0.00 0.00 0.00 2.90
1125 1892 5.193527 TCCTCATAATCAAGGTGGATCCAAA 59.806 40.000 18.20 0.00 39.02 3.28
1166 1933 2.260869 ACACCAACATCGCCTGCAC 61.261 57.895 0.00 0.00 0.00 4.57
1170 1937 2.108514 CAACATCGCCTGCACGGAT 61.109 57.895 6.40 0.00 33.16 4.18
1181 1948 3.576356 CACGGATGGCGATGGCAC 61.576 66.667 1.01 0.00 41.84 5.01
1191 1958 3.520862 GATGGCACCGGCACCATG 61.521 66.667 28.52 9.04 46.72 3.66
1346 2117 4.056125 CGCACCAGTGAGCCGAGA 62.056 66.667 0.99 0.00 0.00 4.04
1367 2138 2.901840 AGGTGTGCGTGCAAGTGG 60.902 61.111 0.59 0.00 0.00 4.00
1379 2150 0.320421 GCAAGTGGGTACGAGCAAGA 60.320 55.000 0.00 0.00 33.55 3.02
1380 2151 1.876416 GCAAGTGGGTACGAGCAAGAA 60.876 52.381 0.00 0.00 33.55 2.52
1385 2156 0.524862 GGGTACGAGCAAGAAGACGA 59.475 55.000 0.00 0.00 0.00 4.20
1409 2182 3.977326 AGGGAAAAGAGAGGAAACTGAGT 59.023 43.478 0.00 0.00 44.43 3.41
1432 2205 3.119637 AGTTGTTGGGAATTAAATCCGCG 60.120 43.478 0.00 0.00 40.62 6.46
1436 2209 0.741915 GGGAATTAAATCCGCGGCAA 59.258 50.000 23.51 12.00 40.62 4.52
1447 2220 1.582610 CCGCGGCAACAATTACCAGT 61.583 55.000 14.67 0.00 0.00 4.00
1475 2248 1.406065 CCAGAGCTCATCCGGTGGAT 61.406 60.000 17.77 0.00 44.21 3.41
1485 2258 2.417516 CGGTGGATGTAGGAGCGG 59.582 66.667 0.00 0.00 0.00 5.52
1486 2259 2.125326 CGGTGGATGTAGGAGCGGA 61.125 63.158 0.00 0.00 0.00 5.54
1503 2276 3.142174 GCGGAAGGATAGAAGGAAATGG 58.858 50.000 0.00 0.00 0.00 3.16
1634 2430 4.323562 GCCGGCCCATCTAGTATTTTAGAT 60.324 45.833 18.11 0.00 40.22 1.98
1635 2431 5.105064 GCCGGCCCATCTAGTATTTTAGATA 60.105 44.000 18.11 0.00 38.11 1.98
1636 2432 6.408206 GCCGGCCCATCTAGTATTTTAGATAT 60.408 42.308 18.11 0.00 38.11 1.63
1638 2434 6.918569 CGGCCCATCTAGTATTTTAGATATCG 59.081 42.308 0.00 0.00 38.11 2.92
1640 2436 7.265673 GCCCATCTAGTATTTTAGATATCGCA 58.734 38.462 0.00 0.00 38.11 5.10
1705 2505 5.859521 GAGACAGACTCTTCGTACTAACA 57.140 43.478 0.00 0.00 41.94 2.41
1724 2524 3.104512 ACAACCAGGCTATGCTACAGTA 58.895 45.455 0.00 0.00 0.00 2.74
2017 2865 7.093992 AGTTGTTGAACTTTTTGGAAATTCGA 58.906 30.769 0.00 0.00 39.56 3.71
2180 3111 8.542497 AAGGTGTTGAACTTTTTAAAAACTCC 57.458 30.769 9.31 9.52 33.50 3.85
2181 3112 7.672240 AGGTGTTGAACTTTTTAAAAACTCCA 58.328 30.769 9.31 4.99 34.96 3.86
2182 3113 8.318412 AGGTGTTGAACTTTTTAAAAACTCCAT 58.682 29.630 9.31 0.00 34.96 3.41
2183 3114 8.387354 GGTGTTGAACTTTTTAAAAACTCCATG 58.613 33.333 9.31 2.04 33.52 3.66
2184 3115 9.145865 GTGTTGAACTTTTTAAAAACTCCATGA 57.854 29.630 9.31 0.00 0.00 3.07
2185 3116 9.712305 TGTTGAACTTTTTAAAAACTCCATGAA 57.288 25.926 9.31 0.00 0.00 2.57
2186 3117 9.967245 GTTGAACTTTTTAAAAACTCCATGAAC 57.033 29.630 9.31 6.34 0.00 3.18
2187 3118 9.936759 TTGAACTTTTTAAAAACTCCATGAACT 57.063 25.926 9.31 0.00 0.00 3.01
2200 3131 9.710900 AAACTCCATGAACTATTTTTCAAATCC 57.289 29.630 0.00 0.00 38.95 3.01
2201 3132 7.538575 ACTCCATGAACTATTTTTCAAATCCG 58.461 34.615 0.00 0.00 38.95 4.18
2202 3133 7.393234 ACTCCATGAACTATTTTTCAAATCCGA 59.607 33.333 0.00 0.00 38.95 4.55
2203 3134 8.292444 TCCATGAACTATTTTTCAAATCCGAT 57.708 30.769 0.00 0.00 38.95 4.18
2204 3135 8.190122 TCCATGAACTATTTTTCAAATCCGATG 58.810 33.333 0.00 0.00 38.95 3.84
2205 3136 8.190122 CCATGAACTATTTTTCAAATCCGATGA 58.810 33.333 0.00 0.00 38.95 2.92
2206 3137 9.571810 CATGAACTATTTTTCAAATCCGATGAA 57.428 29.630 0.00 0.00 38.95 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.434420 TGTGACAACAAAGAAAATTGAAGATTT 57.566 25.926 0.00 0.00 34.38 2.17
26 27 9.603921 ATGTGACAACAAAGAAAATTGAAGATT 57.396 25.926 0.00 0.00 40.46 2.40
60 61 4.586001 AGTTAACTACGTCCCAAAGTCTCA 59.414 41.667 6.26 0.00 0.00 3.27
64 65 8.246871 GTCTATAAGTTAACTACGTCCCAAAGT 58.753 37.037 8.92 0.00 0.00 2.66
87 330 2.916702 TGCATGGATCGCATTAGTCT 57.083 45.000 0.00 0.00 33.55 3.24
150 393 4.267690 GCAAACTTCGGAAAAGGAAAACTG 59.732 41.667 0.00 0.00 0.00 3.16
165 408 6.586844 ACAGAGAGAATACGTTAGCAAACTTC 59.413 38.462 0.00 0.00 33.15 3.01
177 420 2.688446 TGCCCTACACAGAGAGAATACG 59.312 50.000 0.00 0.00 0.00 3.06
189 432 0.463654 TGGATCGCATTGCCCTACAC 60.464 55.000 2.41 0.00 0.00 2.90
203 446 4.630644 TCTCCCAATAGAAGCATGGATC 57.369 45.455 0.00 0.00 36.27 3.36
293 538 5.733620 TGGTCTGTATTTTTCGTACTCCT 57.266 39.130 0.00 0.00 0.00 3.69
308 553 5.624159 TGAGATTGTTCTTCAATGGTCTGT 58.376 37.500 0.00 0.00 45.49 3.41
310 555 7.587037 TTTTGAGATTGTTCTTCAATGGTCT 57.413 32.000 0.00 0.00 45.49 3.85
347 593 7.518848 GCATCTTGATAATCGCTGTTGTATCAA 60.519 37.037 0.00 0.00 39.47 2.57
397 643 6.769512 ACTGTCACAAATAGGTCTGTGTATT 58.230 36.000 2.45 0.00 42.86 1.89
453 699 3.327757 TGGCCTACTTCCATAAGCATAGG 59.672 47.826 3.32 0.00 35.76 2.57
485 731 7.008440 TCAATCAACAATATCAGCTCTTTCG 57.992 36.000 0.00 0.00 0.00 3.46
492 738 6.127925 TGGAACACTCAATCAACAATATCAGC 60.128 38.462 0.00 0.00 0.00 4.26
567 1090 7.069986 TCCAATACTTCTAGGAGTAGCAGATT 58.930 38.462 16.11 3.92 35.72 2.40
572 1095 7.442666 CCAAATTCCAATACTTCTAGGAGTAGC 59.557 40.741 16.11 0.00 35.72 3.58
591 1114 6.730960 ATGTTGATGCATGTTTCCAAATTC 57.269 33.333 2.46 0.00 0.00 2.17
628 1151 9.859427 CAAAGTGTCACATTTGGTATTATTCAT 57.141 29.630 5.62 0.00 33.68 2.57
670 1252 6.106673 TGGCTTGTACTACAGAATAAGCTTC 58.893 40.000 0.00 0.00 40.12 3.86
708 1293 3.820689 TGAACTAAAATGATGCACGCAC 58.179 40.909 0.00 0.00 0.00 5.34
709 1294 4.700268 ATGAACTAAAATGATGCACGCA 57.300 36.364 0.00 0.00 0.00 5.24
710 1295 6.201517 ACATATGAACTAAAATGATGCACGC 58.798 36.000 10.38 0.00 0.00 5.34
711 1296 8.011673 CCTACATATGAACTAAAATGATGCACG 58.988 37.037 10.38 0.00 0.00 5.34
712 1297 9.056005 TCCTACATATGAACTAAAATGATGCAC 57.944 33.333 10.38 0.00 0.00 4.57
713 1298 9.797642 ATCCTACATATGAACTAAAATGATGCA 57.202 29.630 10.38 0.00 0.00 3.96
783 1504 6.923508 TGTATTCGTGATTAGCCATGTCTTAG 59.076 38.462 0.00 0.00 0.00 2.18
858 1584 6.873997 TGTTAGTGGAAGGTGTATATCTGTG 58.126 40.000 0.00 0.00 0.00 3.66
921 1651 4.989279 TTCCTATCCTTTTTCTGCATGC 57.011 40.909 11.82 11.82 0.00 4.06
939 1669 6.813649 GCCTCTCCAATATTTTTCTTGTTTCC 59.186 38.462 0.00 0.00 0.00 3.13
957 1700 2.183679 TCTCTCTTTTCCTGCCTCTCC 58.816 52.381 0.00 0.00 0.00 3.71
984 1747 0.322816 TCATTCTTCCACCTGCAGGC 60.323 55.000 33.06 0.00 39.32 4.85
1059 1822 1.000993 ATCGTGTCTCCCCTGAGCT 59.999 57.895 0.00 0.00 38.58 4.09
1064 1827 1.758514 ATCGCATCGTGTCTCCCCT 60.759 57.895 0.00 0.00 0.00 4.79
1089 1854 4.040829 TGATTATGAGGATGCTGACGGATT 59.959 41.667 0.00 0.00 0.00 3.01
1091 1856 2.965147 TGATTATGAGGATGCTGACGGA 59.035 45.455 0.00 0.00 0.00 4.69
1107 1874 4.599041 CCAGTTTGGATCCACCTTGATTA 58.401 43.478 15.91 0.00 40.96 1.75
1125 1892 3.241530 TTGTCTCCCGCAGCCAGT 61.242 61.111 0.00 0.00 0.00 4.00
1181 1948 2.280389 CGATCTCCATGGTGCCGG 60.280 66.667 12.58 0.00 0.00 6.13
1217 1985 0.392729 CCCAAGGAGAAGCTGCTCAG 60.393 60.000 23.57 11.96 36.62 3.35
1268 2037 1.025113 ACGCCTCGTCGATCTCTCAA 61.025 55.000 0.00 0.00 33.69 3.02
1318 2089 3.673956 CTGGTGCGGCCACGGATTA 62.674 63.158 2.24 0.00 43.94 1.75
1346 2117 2.906388 TTGCACGCACACCTGCAT 60.906 55.556 0.00 0.00 44.50 3.96
1367 2138 1.068748 TGTCGTCTTCTTGCTCGTACC 60.069 52.381 0.00 0.00 0.00 3.34
1379 2150 2.300437 CCTCTCTTTTCCCTGTCGTCTT 59.700 50.000 0.00 0.00 0.00 3.01
1380 2151 1.896465 CCTCTCTTTTCCCTGTCGTCT 59.104 52.381 0.00 0.00 0.00 4.18
1385 2156 3.716872 TCAGTTTCCTCTCTTTTCCCTGT 59.283 43.478 0.00 0.00 0.00 4.00
1409 2182 4.095185 CGCGGATTTAATTCCCAACAACTA 59.905 41.667 10.16 0.00 31.61 2.24
1432 2205 3.254657 TGTTAGCACTGGTAATTGTTGCC 59.745 43.478 4.06 0.00 35.79 4.52
1436 2209 3.081804 GGCTGTTAGCACTGGTAATTGT 58.918 45.455 4.06 0.00 44.75 2.71
1475 2248 3.223435 CTTCTATCCTTCCGCTCCTACA 58.777 50.000 0.00 0.00 0.00 2.74
1477 2250 2.445905 TCCTTCTATCCTTCCGCTCCTA 59.554 50.000 0.00 0.00 0.00 2.94
1485 2258 5.830457 CCCTTTCCATTTCCTTCTATCCTTC 59.170 44.000 0.00 0.00 0.00 3.46
1486 2259 5.341200 CCCCTTTCCATTTCCTTCTATCCTT 60.341 44.000 0.00 0.00 0.00 3.36
1503 2276 3.690460 TGCTCTTTCTTGATCCCCTTTC 58.310 45.455 0.00 0.00 0.00 2.62
1705 2505 3.375699 ACTACTGTAGCATAGCCTGGTT 58.624 45.455 14.55 0.00 36.79 3.67
1724 2524 6.093633 GTGGAAAAGAGTACAACAGTTCAACT 59.906 38.462 0.00 0.00 0.00 3.16
1992 2840 7.093992 TCGAATTTCCAAAAAGTTCAACAACT 58.906 30.769 0.00 0.00 45.43 3.16
1993 2841 7.284518 TCGAATTTCCAAAAAGTTCAACAAC 57.715 32.000 0.00 0.00 0.00 3.32
1994 2842 7.761704 TCATCGAATTTCCAAAAAGTTCAACAA 59.238 29.630 0.00 0.00 0.00 2.83
1995 2843 7.261325 TCATCGAATTTCCAAAAAGTTCAACA 58.739 30.769 0.00 0.00 0.00 3.33
1996 2844 7.692908 TCATCGAATTTCCAAAAAGTTCAAC 57.307 32.000 0.00 0.00 0.00 3.18
1997 2845 7.978975 AGTTCATCGAATTTCCAAAAAGTTCAA 59.021 29.630 0.00 0.00 0.00 2.69
1998 2846 7.488322 AGTTCATCGAATTTCCAAAAAGTTCA 58.512 30.769 0.00 0.00 0.00 3.18
1999 2847 7.930513 AGTTCATCGAATTTCCAAAAAGTTC 57.069 32.000 0.00 0.00 0.00 3.01
2000 2848 9.981114 AATAGTTCATCGAATTTCCAAAAAGTT 57.019 25.926 0.00 0.00 0.00 2.66
2001 2849 9.981114 AAATAGTTCATCGAATTTCCAAAAAGT 57.019 25.926 0.00 0.00 0.00 2.66
2005 2853 9.973450 TGAAAAATAGTTCATCGAATTTCCAAA 57.027 25.926 0.00 0.00 32.56 3.28
2006 2854 9.973450 TTGAAAAATAGTTCATCGAATTTCCAA 57.027 25.926 0.00 0.00 37.36 3.53
2007 2855 9.973450 TTTGAAAAATAGTTCATCGAATTTCCA 57.027 25.926 0.00 0.00 37.36 3.53
2012 2860 8.673711 TCGGATTTGAAAAATAGTTCATCGAAT 58.326 29.630 0.00 4.64 37.36 3.34
2015 2863 8.122330 TCATCGGATTTGAAAAATAGTTCATCG 58.878 33.333 0.00 0.00 37.36 3.84
2017 2865 9.573133 GTTCATCGGATTTGAAAAATAGTTCAT 57.427 29.630 0.00 0.00 37.36 2.57
2079 2928 7.535139 AGTTCATCGAGTTTTGAAAAAGTTCA 58.465 30.769 0.92 0.00 42.12 3.18
2094 2943 7.684670 TCGGATTTGAAAAATAGTTCATCGAG 58.315 34.615 0.00 0.00 37.36 4.04
2154 3085 8.995220 GGAGTTTTTAAAAAGTTCAACACCTTT 58.005 29.630 19.43 0.00 32.00 3.11
2155 3086 8.151596 TGGAGTTTTTAAAAAGTTCAACACCTT 58.848 29.630 22.03 0.00 34.67 3.50
2156 3087 7.672240 TGGAGTTTTTAAAAAGTTCAACACCT 58.328 30.769 22.03 9.79 34.67 4.00
2157 3088 7.892778 TGGAGTTTTTAAAAAGTTCAACACC 57.107 32.000 22.03 16.55 34.67 4.16
2158 3089 9.145865 TCATGGAGTTTTTAAAAAGTTCAACAC 57.854 29.630 26.04 11.89 39.55 3.32
2159 3090 9.712305 TTCATGGAGTTTTTAAAAAGTTCAACA 57.288 25.926 26.04 19.09 39.55 3.33
2160 3091 9.967245 GTTCATGGAGTTTTTAAAAAGTTCAAC 57.033 29.630 26.04 18.46 39.55 3.18
2161 3092 9.936759 AGTTCATGGAGTTTTTAAAAAGTTCAA 57.063 25.926 26.04 15.58 39.55 2.69
2174 3105 9.710900 GGATTTGAAAAATAGTTCATGGAGTTT 57.289 29.630 0.00 0.00 37.36 2.66
2175 3106 8.028938 CGGATTTGAAAAATAGTTCATGGAGTT 58.971 33.333 0.00 0.00 37.36 3.01
2176 3107 7.393234 TCGGATTTGAAAAATAGTTCATGGAGT 59.607 33.333 0.00 0.00 37.36 3.85
2177 3108 7.761409 TCGGATTTGAAAAATAGTTCATGGAG 58.239 34.615 0.00 0.00 37.36 3.86
2178 3109 7.695480 TCGGATTTGAAAAATAGTTCATGGA 57.305 32.000 0.00 0.00 37.36 3.41
2179 3110 8.190122 TCATCGGATTTGAAAAATAGTTCATGG 58.810 33.333 0.00 0.00 37.36 3.66
2180 3111 9.571810 TTCATCGGATTTGAAAAATAGTTCATG 57.428 29.630 0.00 0.00 37.36 3.07


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

AutoCloner maintained by Alex Coulton.