Multiple sequence alignment - TraesCS1A01G188900

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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 TraesCS1A01G188900 chr1A 100.000 3396 0 0 1 3396 341874765 341871370 0.000000e+00 6272
1 TraesCS1A01G188900 chr1D 92.233 2691 103 43 285 2944 258978038 258980653 0.000000e+00 3714
2 TraesCS1A01G188900 chr1D 88.571 385 19 5 2951 3312 258980726 258981108 8.650000e-121 444
3 TraesCS1A01G188900 chr1D 89.899 297 18 2 1705 2001 11506070 11505786 4.140000e-99 372
4 TraesCS1A01G188900 chr1B 90.736 1835 80 22 1613 3396 353946950 353945155 0.000000e+00 2364
5 TraesCS1A01G188900 chr1B 91.589 1403 70 21 257 1631 353948379 353946997 0.000000e+00 1893
6 TraesCS1A01G188900 chr1B 90.103 485 47 1 1273 1756 77720289 77720773 2.220000e-176 628
7 TraesCS1A01G188900 chr1B 90.572 297 16 2 1705 2001 501626699 501626415 1.910000e-102 383
8 TraesCS1A01G188900 chr3B 87.719 570 68 2 1273 1841 104584828 104584260 0.000000e+00 664
9 TraesCS1A01G188900 chr3B 88.546 227 14 2 1705 1931 173329557 173329343 7.230000e-67 265
10 TraesCS1A01G188900 chr5D 91.246 297 14 2 1705 2001 532474284 532474000 8.830000e-106 394
11 TraesCS1A01G188900 chr5D 91.358 243 20 1 1461 1703 532475102 532474861 7.020000e-87 331
12 TraesCS1A01G188900 chr5D 91.304 92 7 1 1266 1356 92290828 92290919 1.280000e-24 124
13 TraesCS1A01G188900 chr2B 90.476 294 16 5 1705 1998 12311926 12312207 8.900000e-101 377
14 TraesCS1A01G188900 chr2B 89.456 294 19 2 1705 1998 295697931 295698212 8.960000e-96 361
15 TraesCS1A01G188900 chr2B 88.745 231 25 1 11 241 225363307 225363078 7.170000e-72 281
16 TraesCS1A01G188900 chrUn 90.136 294 17 2 1705 1998 227390969 227391250 4.140000e-99 372
17 TraesCS1A01G188900 chrUn 89.899 297 18 2 1705 2001 241176120 241175836 4.140000e-99 372
18 TraesCS1A01G188900 chr7B 89.899 297 18 2 1705 2001 71219438 71219154 4.140000e-99 372
19 TraesCS1A01G188900 chr7B 89.562 297 19 2 1705 2001 413036744 413036460 1.930000e-97 366
20 TraesCS1A01G188900 chr7A 89.899 297 18 2 1705 2001 682818976 682818692 4.140000e-99 372
21 TraesCS1A01G188900 chr7A 90.217 92 7 2 1266 1355 626867058 626867149 5.950000e-23 119
22 TraesCS1A01G188900 chr5B 89.899 297 18 2 1705 2001 295931653 295931369 4.140000e-99 372
23 TraesCS1A01G188900 chr5B 89.720 107 11 0 1274 1380 163656197 163656091 1.640000e-28 137
24 TraesCS1A01G188900 chr4D 93.827 243 14 1 1461 1703 505944919 505945160 6.930000e-97 364
25 TraesCS1A01G188900 chr4D 92.373 236 17 1 7 242 343547139 343546905 5.430000e-88 335
26 TraesCS1A01G188900 chr4D 79.851 268 44 8 1931 2193 502578366 502578104 1.610000e-43 187
27 TraesCS1A01G188900 chr4A 87.547 265 30 3 1333 1595 738692920 738693183 1.530000e-78 303
28 TraesCS1A01G188900 chr4A 88.400 250 27 2 1333 1580 493269967 493269718 1.980000e-77 300
29 TraesCS1A01G188900 chr5A 88.400 250 27 2 1333 1580 671854365 671854614 1.980000e-77 300
30 TraesCS1A01G188900 chr5A 87.815 238 27 2 7 243 649622479 649622715 9.280000e-71 278
31 TraesCS1A01G188900 chr5A 87.395 238 28 2 7 243 649620461 649620697 4.320000e-69 272
32 TraesCS1A01G188900 chr5A 79.851 268 44 8 1931 2193 685996368 685996106 1.610000e-43 187
33 TraesCS1A01G188900 chr5A 89.130 92 8 2 1266 1355 562124159 562124068 2.770000e-21 113
34 TraesCS1A01G188900 chr4B 88.797 241 26 1 1 241 617289373 617289134 9.220000e-76 294
35 TraesCS1A01G188900 chr4B 81.034 174 31 2 1646 1818 646974948 646974776 1.640000e-28 137
36 TraesCS1A01G188900 chr7D 88.841 233 26 0 9 241 28856439 28856207 1.540000e-73 287
37 TraesCS1A01G188900 chr7D 91.304 92 7 1 1266 1356 592034581 592034672 1.280000e-24 124
38 TraesCS1A01G188900 chr3A 88.066 243 27 2 1461 1703 604763450 604763690 1.540000e-73 287
39 TraesCS1A01G188900 chr6B 88.841 233 25 1 9 241 191515402 191515171 5.550000e-73 285
40 TraesCS1A01G188900 chr6B 88.412 233 27 0 9 241 56968368 56968136 7.170000e-72 281
41 TraesCS1A01G188900 chr6B 87.764 237 28 1 7 242 191372230 191371994 3.340000e-70 276
42 TraesCS1A01G188900 chr2A 85.887 248 34 1 1333 1579 595476191 595476438 2.600000e-66 263
43 TraesCS1A01G188900 chr6A 94.845 97 5 0 1197 1293 585206274 585206370 5.870000e-33 152


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 TraesCS1A01G188900 chr1A 341871370 341874765 3395 True 6272.0 6272 100.0000 1 3396 1 chr1A.!!$R1 3395
1 TraesCS1A01G188900 chr1D 258978038 258981108 3070 False 2079.0 3714 90.4020 285 3312 2 chr1D.!!$F1 3027
2 TraesCS1A01G188900 chr1B 353945155 353948379 3224 True 2128.5 2364 91.1625 257 3396 2 chr1B.!!$R2 3139
3 TraesCS1A01G188900 chr3B 104584260 104584828 568 True 664.0 664 87.7190 1273 1841 1 chr3B.!!$R1 568
4 TraesCS1A01G188900 chr5D 532474000 532475102 1102 True 362.5 394 91.3020 1461 2001 2 chr5D.!!$R1 540
5 TraesCS1A01G188900 chr5A 649620461 649622715 2254 False 275.0 278 87.6050 7 243 2 chr5A.!!$F2 236

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
917 2040 0.109412 CCGTTACCACTCTCCACGAC 60.109 60.0 0.00 0.0 32.51 4.34 F
1600 2821 0.178973 TCTCCGGAACTGACACTCCA 60.179 55.0 5.23 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 4198 0.035343 GTCCAGAGCCCACCTAAACC 60.035 60.0 0.00 0.0 0.00 3.27 R
3086 5180 1.458639 GGGCCATAGGTGCATTGAGC 61.459 60.0 4.39 0.0 45.96 4.26 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
43 44 9.253832 TCATATGGTTTGGTGATAACAGAAATT 57.746 29.630 2.13 0.00 0.00 1.82
47 48 8.472007 TGGTTTGGTGATAACAGAAATTAAGT 57.528 30.769 0.00 0.00 0.00 2.24
59 60 5.977129 ACAGAAATTAAGTTGCGTTCTTTGG 59.023 36.000 0.00 0.00 0.00 3.28
60 61 6.183360 ACAGAAATTAAGTTGCGTTCTTTGGA 60.183 34.615 0.00 0.00 0.00 3.53
63 64 7.926018 AGAAATTAAGTTGCGTTCTTTGGATTT 59.074 29.630 0.00 0.00 0.00 2.17
75 76 9.952341 GCGTTCTTTGGATTTTATTTGTAATTC 57.048 29.630 0.00 0.00 0.00 2.17
79 80 9.849166 TCTTTGGATTTTATTTGTAATTCCGTC 57.151 29.630 0.00 0.00 31.01 4.79
97 98 3.554324 CCGTCTTTGAAAGTCGTTCTTCA 59.446 43.478 19.63 0.00 38.16 3.02
140 141 9.710979 GTTTAGCTAAGCATATACTATCTCTCG 57.289 37.037 14.73 0.00 0.00 4.04
148 149 0.536687 TACTATCTCTCGGTGCGGGG 60.537 60.000 0.00 0.00 0.00 5.73
149 150 3.214250 CTATCTCTCGGTGCGGGGC 62.214 68.421 0.00 0.00 0.00 5.80
181 182 4.164843 GTTGGCTAACCCTCATAATCCA 57.835 45.455 0.62 0.00 33.59 3.41
184 185 5.402054 TGGCTAACCCTCATAATCCAAAT 57.598 39.130 0.00 0.00 33.59 2.32
202 203 5.192722 TCCAAATTGTATCCCACTCCATGTA 59.807 40.000 0.00 0.00 0.00 2.29
203 204 6.070656 CCAAATTGTATCCCACTCCATGTAT 58.929 40.000 0.00 0.00 0.00 2.29
241 242 6.901081 AGCTTAGCTTTGTCCTACAAAAAT 57.099 33.333 0.00 1.76 46.15 1.82
242 243 7.996098 AGCTTAGCTTTGTCCTACAAAAATA 57.004 32.000 0.00 0.95 46.15 1.40
243 244 8.581253 AGCTTAGCTTTGTCCTACAAAAATAT 57.419 30.769 0.00 0.00 46.15 1.28
244 245 8.462016 AGCTTAGCTTTGTCCTACAAAAATATG 58.538 33.333 0.00 6.14 46.15 1.78
245 246 7.702348 GCTTAGCTTTGTCCTACAAAAATATGG 59.298 37.037 6.67 0.00 46.15 2.74
246 247 6.530019 AGCTTTGTCCTACAAAAATATGGG 57.470 37.500 6.67 0.00 46.15 4.00
247 248 5.422012 AGCTTTGTCCTACAAAAATATGGGG 59.578 40.000 6.67 0.00 46.15 4.96
248 249 5.186992 GCTTTGTCCTACAAAAATATGGGGT 59.813 40.000 6.67 0.00 46.15 4.95
250 251 5.522315 TGTCCTACAAAAATATGGGGTCA 57.478 39.130 0.00 0.00 0.00 4.02
251 252 5.893500 TGTCCTACAAAAATATGGGGTCAA 58.106 37.500 0.00 0.00 0.00 3.18
252 253 6.315714 TGTCCTACAAAAATATGGGGTCAAA 58.684 36.000 0.00 0.00 0.00 2.69
253 254 6.435904 TGTCCTACAAAAATATGGGGTCAAAG 59.564 38.462 0.00 0.00 0.00 2.77
255 256 4.551702 ACAAAAATATGGGGTCAAAGCC 57.448 40.909 0.00 0.00 34.31 4.35
292 293 6.414732 CACAATCTCTACTTTTGGGGACATA 58.585 40.000 0.00 0.00 42.32 2.29
419 1524 0.609151 TTTTCATGGCCATGCACAGG 59.391 50.000 36.47 15.96 38.65 4.00
438 1543 4.891756 ACAGGCATTCAGCTAGCATTATTT 59.108 37.500 18.83 0.00 44.79 1.40
473 1578 9.260002 GTCAATTCATTCCAAAAGTGTTTACAT 57.740 29.630 0.00 0.00 0.00 2.29
503 1608 2.486191 GGGCAGGTGATAACTCATGGAG 60.486 54.545 0.00 0.00 32.98 3.86
557 1662 2.890474 GCACACCGTATGCCCGAG 60.890 66.667 0.00 0.00 37.08 4.63
628 1733 4.043200 GCTCGGCCACAAGGTTGC 62.043 66.667 2.24 0.00 37.19 4.17
629 1734 3.365265 CTCGGCCACAAGGTTGCC 61.365 66.667 2.24 1.61 40.41 4.52
833 1956 2.904866 GAGGCAAACGCACCACCA 60.905 61.111 0.00 0.00 0.00 4.17
856 1979 1.103398 GCTGCGCCATTTATCACCCT 61.103 55.000 4.18 0.00 0.00 4.34
896 2019 1.378119 CCTTTTCCACTACCCCGCC 60.378 63.158 0.00 0.00 0.00 6.13
917 2040 0.109412 CCGTTACCACTCTCCACGAC 60.109 60.000 0.00 0.00 32.51 4.34
982 2116 3.450115 GACAGCTCGCTACCCCGT 61.450 66.667 0.00 0.00 0.00 5.28
1120 2255 4.429212 CGTGGATCGTGCCGGTCA 62.429 66.667 1.90 0.00 38.92 4.02
1126 2261 2.607668 GATCGTGCCGGTCATCGTGA 62.608 60.000 1.90 0.03 36.93 4.35
1416 2627 3.243873 TGTCGTCTTCAGATTGCAGAAGT 60.244 43.478 11.81 0.00 41.46 3.01
1424 2635 1.589716 GATTGCAGAAGTTGGGCGCT 61.590 55.000 7.64 0.00 0.00 5.92
1475 2686 2.567049 GGGTGGAGACTCGTGACG 59.433 66.667 0.00 0.00 0.00 4.35
1600 2821 0.178973 TCTCCGGAACTGACACTCCA 60.179 55.000 5.23 0.00 0.00 3.86
1642 2928 6.194796 ACTGATATTGTTCCCGTCAATTTG 57.805 37.500 0.00 0.00 36.92 2.32
1716 3577 4.264253 GTGATGTCATCCCTGTTCATCAA 58.736 43.478 10.36 0.00 41.38 2.57
1841 3702 2.416431 GCATCTCCAACCAATTCTGCAC 60.416 50.000 0.00 0.00 0.00 4.57
1842 3703 2.655090 TCTCCAACCAATTCTGCACA 57.345 45.000 0.00 0.00 0.00 4.57
1843 3704 3.159213 TCTCCAACCAATTCTGCACAT 57.841 42.857 0.00 0.00 0.00 3.21
1844 3705 4.299586 TCTCCAACCAATTCTGCACATA 57.700 40.909 0.00 0.00 0.00 2.29
1845 3706 4.858850 TCTCCAACCAATTCTGCACATAT 58.141 39.130 0.00 0.00 0.00 1.78
1846 3707 5.263599 TCTCCAACCAATTCTGCACATATT 58.736 37.500 0.00 0.00 0.00 1.28
1847 3708 5.357878 TCTCCAACCAATTCTGCACATATTC 59.642 40.000 0.00 0.00 0.00 1.75
1848 3709 5.263599 TCCAACCAATTCTGCACATATTCT 58.736 37.500 0.00 0.00 0.00 2.40
1849 3710 5.125900 TCCAACCAATTCTGCACATATTCTG 59.874 40.000 0.00 0.00 0.00 3.02
1850 3711 4.644103 ACCAATTCTGCACATATTCTGC 57.356 40.909 0.00 0.00 35.03 4.26
1851 3712 4.018490 ACCAATTCTGCACATATTCTGCA 58.982 39.130 5.01 5.01 42.42 4.41
2224 4198 4.273480 ACGACATCTTTCTTGTTGAGTTGG 59.727 41.667 0.00 0.00 33.50 3.77
2249 4223 3.706373 TGGGCTCTGGACTTCCGC 61.706 66.667 0.00 0.00 39.43 5.54
2392 4366 1.523258 CAGATGGAGCTGCGGGAAG 60.523 63.158 0.00 0.00 0.00 3.46
2415 4389 0.883833 AATGGGAGCAAGCAACTTCG 59.116 50.000 0.00 0.00 0.00 3.79
2482 4456 3.119495 TGCGCAGATGCTGTATATACGAT 60.119 43.478 5.66 0.63 39.32 3.73
2483 4457 4.095782 TGCGCAGATGCTGTATATACGATA 59.904 41.667 5.66 0.00 39.32 2.92
2484 4458 5.215903 GCGCAGATGCTGTATATACGATAT 58.784 41.667 0.30 2.44 39.32 1.63
2485 4459 5.116225 GCGCAGATGCTGTATATACGATATG 59.884 44.000 0.30 8.45 39.32 1.78
2486 4460 6.430451 CGCAGATGCTGTATATACGATATGA 58.570 40.000 8.33 0.00 39.32 2.15
2503 4477 6.817140 ACGATATGAGTACTGCTATATGACGA 59.183 38.462 0.00 0.00 0.00 4.20
2530 4504 0.179092 CCCGGGGTTTACTCGATGAC 60.179 60.000 14.71 0.00 0.00 3.06
2559 4533 5.513495 TCGTTCGGTTGTTTGATTTGAAAAG 59.487 36.000 0.00 0.00 0.00 2.27
2616 4590 0.748005 ACAGCGCGGATGCCTTTTAT 60.748 50.000 16.26 0.00 38.08 1.40
2795 4776 4.414852 CGAAAGCAAGTGGTAATGAATGG 58.585 43.478 0.00 0.00 0.00 3.16
2875 4877 2.507547 CAAGCGCGGCGGTAGTAA 60.508 61.111 28.08 0.00 36.27 2.24
2903 4905 4.901627 GCGACAGCACACAAACTC 57.098 55.556 0.00 0.00 44.35 3.01
2910 4912 4.611355 CGACAGCACACAAACTCCAAATAG 60.611 45.833 0.00 0.00 0.00 1.73
2944 4946 6.418057 AAACTCCAAAATGAATGCCAGTAA 57.582 33.333 0.00 0.00 0.00 2.24
2945 4947 6.610075 AACTCCAAAATGAATGCCAGTAAT 57.390 33.333 0.00 0.00 0.00 1.89
2946 4948 7.716799 AACTCCAAAATGAATGCCAGTAATA 57.283 32.000 0.00 0.00 0.00 0.98
2947 4949 7.716799 ACTCCAAAATGAATGCCAGTAATAA 57.283 32.000 0.00 0.00 0.00 1.40
3000 5071 1.218047 GACGTGCATGGCAGGAGTA 59.782 57.895 16.65 0.00 45.68 2.59
3086 5180 4.033932 TGGCACGAATCATCACTAAAATCG 59.966 41.667 0.00 0.00 35.16 3.34
3099 5193 4.332543 CACTAAAATCGCTCAATGCACCTA 59.667 41.667 0.00 0.00 43.06 3.08
3204 5298 3.262660 TCAGAAGCATGGACTTGACATCT 59.737 43.478 0.00 0.00 0.00 2.90
3329 5423 8.345565 AGCCTGCATATAAATTAAAGAAACGAG 58.654 33.333 0.00 0.00 0.00 4.18
3347 5441 3.873952 ACGAGAAGATCAGCAAATTAGCC 59.126 43.478 0.00 0.00 34.23 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.289160 TGATCCCTGGTTGCTAAGCT 58.711 50.000 0.00 0.00 0.00 3.74
1 2 2.355010 ATGATCCCTGGTTGCTAAGC 57.645 50.000 0.00 0.00 0.00 3.09
2 3 4.202503 ACCATATGATCCCTGGTTGCTAAG 60.203 45.833 3.65 0.00 40.34 2.18
3 4 3.721575 ACCATATGATCCCTGGTTGCTAA 59.278 43.478 3.65 0.00 40.34 3.09
4 5 3.326521 ACCATATGATCCCTGGTTGCTA 58.673 45.455 3.65 0.00 40.34 3.49
5 6 2.138542 ACCATATGATCCCTGGTTGCT 58.861 47.619 3.65 0.00 40.34 3.91
10 11 3.117550 TCACCAAACCATATGATCCCTGG 60.118 47.826 3.65 6.08 36.09 4.45
25 26 7.593273 CGCAACTTAATTTCTGTTATCACCAAA 59.407 33.333 0.00 0.00 0.00 3.28
27 28 6.205853 ACGCAACTTAATTTCTGTTATCACCA 59.794 34.615 0.00 0.00 0.00 4.17
43 44 8.973378 CAAATAAAATCCAAAGAACGCAACTTA 58.027 29.630 0.00 0.00 0.00 2.24
47 48 8.873215 TTACAAATAAAATCCAAAGAACGCAA 57.127 26.923 0.00 0.00 0.00 4.85
63 64 9.887406 GACTTTCAAAGACGGAATTACAAATAA 57.113 29.630 3.49 0.00 0.00 1.40
79 80 4.728608 CCGTTTGAAGAACGACTTTCAAAG 59.271 41.667 18.57 0.00 45.64 2.77
97 98 4.392138 GCTAAACTATGAGCTTCACCGTTT 59.608 41.667 13.64 13.64 36.61 3.60
128 129 1.535833 CCCGCACCGAGAGATAGTAT 58.464 55.000 0.00 0.00 0.00 2.12
129 130 0.536687 CCCCGCACCGAGAGATAGTA 60.537 60.000 0.00 0.00 0.00 1.82
172 173 7.004086 GGAGTGGGATACAATTTGGATTATGA 58.996 38.462 0.78 0.00 39.74 2.15
184 185 9.332713 TCATAATATACATGGAGTGGGATACAA 57.667 33.333 0.00 0.00 39.74 2.41
234 235 3.263170 GGGCTTTGACCCCATATTTTTGT 59.737 43.478 0.00 0.00 45.00 2.83
235 236 3.872696 GGGCTTTGACCCCATATTTTTG 58.127 45.455 0.00 0.00 45.00 2.44
246 247 3.321968 GGAATTATGGATGGGCTTTGACC 59.678 47.826 0.00 0.00 0.00 4.02
247 248 3.960102 TGGAATTATGGATGGGCTTTGAC 59.040 43.478 0.00 0.00 0.00 3.18
248 249 3.960102 GTGGAATTATGGATGGGCTTTGA 59.040 43.478 0.00 0.00 0.00 2.69
250 251 3.992999 TGTGGAATTATGGATGGGCTTT 58.007 40.909 0.00 0.00 0.00 3.51
251 252 3.686227 TGTGGAATTATGGATGGGCTT 57.314 42.857 0.00 0.00 0.00 4.35
252 253 3.686227 TTGTGGAATTATGGATGGGCT 57.314 42.857 0.00 0.00 0.00 5.19
253 254 4.154942 AGATTGTGGAATTATGGATGGGC 58.845 43.478 0.00 0.00 0.00 5.36
255 256 7.456725 AGTAGAGATTGTGGAATTATGGATGG 58.543 38.462 0.00 0.00 0.00 3.51
260 261 8.408601 CCCAAAAGTAGAGATTGTGGAATTATG 58.591 37.037 0.00 0.00 0.00 1.90
292 293 4.853468 TCACATGTCCTCTAGAGAGTCT 57.147 45.455 21.76 0.00 40.48 3.24
413 1518 1.028330 TGCTAGCTGAATGCCTGTGC 61.028 55.000 17.23 0.00 44.23 4.57
417 1522 5.009410 GTCAAATAATGCTAGCTGAATGCCT 59.991 40.000 17.23 0.00 44.23 4.75
419 1524 4.908156 CGTCAAATAATGCTAGCTGAATGC 59.092 41.667 17.23 0.00 43.29 3.56
420 1525 6.291067 TCGTCAAATAATGCTAGCTGAATG 57.709 37.500 17.23 7.74 0.00 2.67
422 1527 4.271049 GCTCGTCAAATAATGCTAGCTGAA 59.729 41.667 17.23 0.83 0.00 3.02
452 1557 6.239458 GGGGATGTAAACACTTTTGGAATGAA 60.239 38.462 0.00 0.00 0.00 2.57
487 1592 4.841246 ACTATCCCTCCATGAGTTATCACC 59.159 45.833 0.00 0.00 38.57 4.02
503 1608 1.327690 TGTCGGGCAGTCACTATCCC 61.328 60.000 4.53 4.53 35.42 3.85
620 1725 0.039527 GTAAACGGCAGGCAACCTTG 60.040 55.000 0.00 0.00 37.17 3.61
625 1730 0.107831 AGACAGTAAACGGCAGGCAA 59.892 50.000 0.00 0.00 0.00 4.52
627 1732 1.356938 GTAGACAGTAAACGGCAGGC 58.643 55.000 0.00 0.00 0.00 4.85
628 1733 1.625616 CGTAGACAGTAAACGGCAGG 58.374 55.000 0.13 0.00 33.13 4.85
785 1907 0.171903 GTGGACGCGGTTTAGCTCTA 59.828 55.000 12.47 0.00 34.40 2.43
786 1908 1.080025 GTGGACGCGGTTTAGCTCT 60.080 57.895 12.47 0.00 34.40 4.09
787 1909 2.098831 GGTGGACGCGGTTTAGCTC 61.099 63.158 12.47 0.00 34.40 4.09
839 1962 1.383456 GCAGGGTGATAAATGGCGCA 61.383 55.000 10.83 0.00 0.00 6.09
896 2019 1.445582 GTGGAGAGTGGTAACGGCG 60.446 63.158 4.80 4.80 42.51 6.46
917 2040 2.240500 GCTCTAATCGGCTGCGGTG 61.241 63.158 7.10 0.00 0.00 4.94
1022 2157 2.291043 GCCTTCTCCTTCCGGTCCA 61.291 63.158 0.00 0.00 0.00 4.02
1120 2255 2.431942 GACGTTGGCGGTCACGAT 60.432 61.111 10.59 0.00 44.60 3.73
1154 2289 0.871722 GCAGTTGTTGGCGTACATCA 59.128 50.000 0.00 0.00 0.00 3.07
1416 2627 4.680237 CCACACGAGAGCGCCCAA 62.680 66.667 2.29 0.00 42.48 4.12
1424 2635 1.745890 CACCTTGTCCCACACGAGA 59.254 57.895 0.00 0.00 38.72 4.04
1475 2686 3.503363 GCGTGGAGCCAGATGCAC 61.503 66.667 0.00 0.00 44.83 4.57
1511 2722 2.362120 AGGCTGAGCATGTTGGCC 60.362 61.111 6.82 12.99 42.74 5.36
1580 2801 1.187087 GGAGTGTCAGTTCCGGAGAT 58.813 55.000 3.34 0.00 0.00 2.75
1600 2821 9.911788 ATATCAGTTCAGAATGTTCAGGTAATT 57.088 29.630 0.00 0.00 37.40 1.40
1642 2928 2.029844 GCCGACTCTCACTGCAACC 61.030 63.158 0.00 0.00 0.00 3.77
1716 3577 0.321653 GCCCACGGAGATGTTGTCTT 60.322 55.000 0.00 0.00 37.29 3.01
1777 3638 0.687354 TCCAGTTGGTGAAGAGCTCC 59.313 55.000 10.93 0.00 36.34 4.70
1841 3702 1.869774 TGCTACCGCTGCAGAATATG 58.130 50.000 20.43 4.98 35.31 1.78
1850 3711 2.816958 CTGGTGCTGCTACCGCTG 60.817 66.667 13.83 5.89 43.87 5.18
1851 3712 4.767255 GCTGGTGCTGCTACCGCT 62.767 66.667 19.44 0.00 43.87 5.52
2048 3924 2.398429 CGCATGAGCAGCACGAAG 59.602 61.111 0.00 0.00 42.27 3.79
2210 4184 4.642885 CACCTAAACCCAACTCAACAAGAA 59.357 41.667 0.00 0.00 0.00 2.52
2224 4198 0.035343 GTCCAGAGCCCACCTAAACC 60.035 60.000 0.00 0.00 0.00 3.27
2249 4223 1.472878 AGCAATGCAGCATCAGTCAAG 59.527 47.619 8.77 0.00 36.85 3.02
2392 4366 1.615392 AGTTGCTTGCTCCCATTTCAC 59.385 47.619 0.00 0.00 0.00 3.18
2483 4457 8.793592 TGTAATTCGTCATATAGCAGTACTCAT 58.206 33.333 0.00 0.00 0.00 2.90
2484 4458 8.074370 GTGTAATTCGTCATATAGCAGTACTCA 58.926 37.037 0.00 0.00 0.00 3.41
2485 4459 7.537991 GGTGTAATTCGTCATATAGCAGTACTC 59.462 40.741 0.00 0.00 0.00 2.59
2486 4460 7.368833 GGTGTAATTCGTCATATAGCAGTACT 58.631 38.462 0.00 0.00 0.00 2.73
2530 4504 3.392769 TCAAACAACCGAACGAAACAG 57.607 42.857 0.00 0.00 0.00 3.16
2606 4580 5.674052 TGGCACACAAATATAAAAGGCAT 57.326 34.783 0.00 0.00 0.00 4.40
2616 4590 8.665471 AAGATGGATCTGTTTGGCACACAAATA 61.665 37.037 7.98 0.00 42.68 1.40
2666 4640 5.066375 TCAAAGCTGTACCATGCATGATAAC 59.934 40.000 28.31 20.47 0.00 1.89
2673 4647 2.857186 TCTCAAAGCTGTACCATGCA 57.143 45.000 0.00 0.00 0.00 3.96
2795 4776 3.049912 GGAATCGCTTTGGTTGTGAAAC 58.950 45.455 0.00 0.00 37.35 2.78
2868 4870 6.529463 TGTCGCTTTTAACAGTTTACTACC 57.471 37.500 0.00 0.00 0.00 3.18
2875 4877 2.680841 TGTGCTGTCGCTTTTAACAGTT 59.319 40.909 4.62 0.00 43.82 3.16
2903 4905 7.270047 TGGAGTTTTCGTATAGACCTATTTGG 58.730 38.462 0.00 0.00 42.93 3.28
2910 4912 7.605410 TCATTTTGGAGTTTTCGTATAGACC 57.395 36.000 0.00 0.00 0.00 3.85
3035 5128 4.206477 AGTGTTTCATGTCATGATCGGA 57.794 40.909 16.19 0.00 39.39 4.55
3036 5129 4.392754 TCAAGTGTTTCATGTCATGATCGG 59.607 41.667 16.19 3.30 39.39 4.18
3037 5130 5.121298 AGTCAAGTGTTTCATGTCATGATCG 59.879 40.000 16.19 1.39 39.39 3.69
3086 5180 1.458639 GGGCCATAGGTGCATTGAGC 61.459 60.000 4.39 0.00 45.96 4.26
3099 5193 1.497309 TTCTCCTTGGTTCGGGCCAT 61.497 55.000 4.39 0.00 38.48 4.40
3204 5298 3.326006 AGACTGGCAATGAGTTTGAGAGA 59.674 43.478 0.00 0.00 37.53 3.10
3249 5343 1.674322 CCACGCCGACCAAAGGAAT 60.674 57.895 0.00 0.00 0.00 3.01
3329 5423 3.243334 GCAGGGCTAATTTGCTGATCTTC 60.243 47.826 11.61 0.00 35.05 2.87


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

AutoCloner maintained by Alex Coulton.