Multiple sequence alignment - TraesCS5B01G094000

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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 TraesCS5B01G094000 chr5B 100.000 3038 0 0 1 3038 123438952 123435915 0.000000e+00 5611.0
1 TraesCS5B01G094000 chr5B 98.109 2009 36 2 1031 3038 123219873 123217866 0.000000e+00 3498.0
2 TraesCS5B01G094000 chr5B 96.337 1283 32 12 1377 2655 123014109 123012838 0.000000e+00 2095.0
3 TraesCS5B01G094000 chr5B 90.513 1033 84 6 1043 2062 88340259 88341290 0.000000e+00 1352.0
4 TraesCS5B01G094000 chr5B 90.772 661 51 9 1 659 123024838 123024186 0.000000e+00 874.0
5 TraesCS5B01G094000 chr5B 90.758 660 51 7 2 659 123222230 123221579 0.000000e+00 872.0
6 TraesCS5B01G094000 chr5B 85.354 792 86 12 1257 2040 88211463 88212232 0.000000e+00 793.0
7 TraesCS5B01G094000 chr5B 90.598 351 33 0 1031 1381 123022482 123022132 1.650000e-127 466.0
8 TraesCS5B01G094000 chr5B 81.903 536 56 17 759 1263 88210770 88211295 6.060000e-112 414.0
9 TraesCS5B01G094000 chr5B 90.533 169 6 4 660 827 123022822 123022663 6.600000e-52 215.0
10 TraesCS5B01G094000 chr5B 89.349 169 8 4 660 827 123220213 123220054 1.430000e-48 204.0
11 TraesCS5B01G094000 chr5B 90.698 86 5 3 2560 2643 250223299 250223215 8.900000e-21 111.0
12 TraesCS5B01G094000 chr5D 88.941 1275 106 19 892 2133 78503820 78505092 0.000000e+00 1541.0
13 TraesCS5B01G094000 chr5D 91.900 642 52 0 1029 1670 78594516 78595157 0.000000e+00 898.0
14 TraesCS5B01G094000 chr5D 85.600 750 94 9 1303 2040 78371229 78371976 0.000000e+00 774.0
15 TraesCS5B01G094000 chr5D 87.745 408 48 2 1662 2068 78602935 78603341 2.740000e-130 475.0
16 TraesCS5B01G094000 chr5D 83.301 509 48 19 830 1306 78361613 78362116 4.650000e-118 435.0
17 TraesCS5B01G094000 chr5D 81.208 298 44 10 270 559 62530312 62530019 2.360000e-56 230.0
18 TraesCS5B01G094000 chr5D 85.135 222 15 8 860 1068 78594303 78594519 8.530000e-51 211.0
19 TraesCS5B01G094000 chr5D 79.348 276 39 11 2380 2642 37662002 37662272 8.660000e-41 178.0
20 TraesCS5B01G094000 chr5D 88.889 54 5 1 2623 2676 216058034 216058086 7.030000e-07 65.8
21 TraesCS5B01G094000 chr5A 91.339 1016 83 4 1029 2040 74863160 74864174 0.000000e+00 1384.0
22 TraesCS5B01G094000 chr5A 96.571 175 6 0 894 1068 74862989 74863163 1.070000e-74 291.0
23 TraesCS5B01G094000 chr5A 93.750 144 9 0 2677 2820 604994115 604994258 1.830000e-52 217.0
24 TraesCS5B01G094000 chr5A 80.435 138 18 8 121 254 548216106 548215974 2.490000e-16 97.1
25 TraesCS5B01G094000 chr7A 97.248 218 6 0 2821 3038 211292414 211292197 1.330000e-98 370.0
26 TraesCS5B01G094000 chr7A 80.435 138 18 8 121 254 607753075 607752943 2.490000e-16 97.1
27 TraesCS5B01G094000 chr4D 97.248 218 6 0 2821 3038 123508047 123508264 1.330000e-98 370.0
28 TraesCS5B01G094000 chr4D 97.248 218 6 0 2821 3038 123737543 123737760 1.330000e-98 370.0
29 TraesCS5B01G094000 chr4D 96.789 218 7 0 2821 3038 123654746 123654963 6.190000e-97 364.0
30 TraesCS5B01G094000 chr2B 97.248 218 6 0 2821 3038 357244934 357245151 1.330000e-98 370.0
31 TraesCS5B01G094000 chr2B 75.926 216 33 15 2383 2592 558009366 558009164 3.230000e-15 93.5
32 TraesCS5B01G094000 chr1D 97.248 218 6 0 2821 3038 212467754 212467971 1.330000e-98 370.0
33 TraesCS5B01G094000 chr1D 80.374 214 26 11 2439 2642 462387478 462387685 6.790000e-32 148.0
34 TraesCS5B01G094000 chr6B 96.789 218 7 0 2821 3038 215728380 215728597 6.190000e-97 364.0
35 TraesCS5B01G094000 chr6B 82.292 288 42 7 295 576 662144864 662145148 1.090000e-59 241.0
36 TraesCS5B01G094000 chr6B 80.000 105 11 4 1619 1723 671658525 671658619 5.430000e-08 69.4
37 TraesCS5B01G094000 chr3B 96.789 218 7 0 2821 3038 39816880 39816663 6.190000e-97 364.0
38 TraesCS5B01G094000 chr3B 95.000 40 2 0 2636 2675 733416119 733416158 2.530000e-06 63.9
39 TraesCS5B01G094000 chr4A 82.201 309 47 6 274 576 575005468 575005162 3.000000e-65 259.0
40 TraesCS5B01G094000 chr4A 77.953 254 42 10 2395 2642 45737104 45737349 2.440000e-31 147.0
41 TraesCS5B01G094000 chr4A 77.907 258 37 13 2398 2642 589470866 589471116 3.160000e-30 143.0
42 TraesCS5B01G094000 chr4A 79.381 194 28 8 2388 2576 45467227 45467041 3.180000e-25 126.0
43 TraesCS5B01G094000 chr4A 82.645 121 13 7 137 254 426686878 426686763 1.930000e-17 100.0
44 TraesCS5B01G094000 chr4A 81.890 127 14 8 132 254 93131560 93131681 6.930000e-17 99.0
45 TraesCS5B01G094000 chr3D 84.173 278 29 10 2372 2642 517012054 517011785 3.890000e-64 255.0
46 TraesCS5B01G094000 chr3D 93.056 144 10 0 2677 2820 202633229 202633086 8.530000e-51 211.0
47 TraesCS5B01G094000 chr3D 79.137 278 35 13 2376 2642 126385816 126385551 1.450000e-38 171.0
48 TraesCS5B01G094000 chr3D 79.213 178 24 10 83 254 172858300 172858130 8.900000e-21 111.0
49 TraesCS5B01G094000 chr2D 81.230 309 49 8 274 576 164743265 164742960 1.090000e-59 241.0
50 TraesCS5B01G094000 chrUn 82.500 280 41 6 271 544 33187441 33187718 3.910000e-59 239.0
51 TraesCS5B01G094000 chrUn 93.056 144 10 0 2677 2820 206793358 206793215 8.530000e-51 211.0
52 TraesCS5B01G094000 chrUn 93.056 144 10 0 2677 2820 246706002 246705859 8.530000e-51 211.0
53 TraesCS5B01G094000 chrUn 93.056 144 10 0 2677 2820 266186159 266186016 8.530000e-51 211.0
54 TraesCS5B01G094000 chrUn 93.056 144 10 0 2677 2820 432754936 432754793 8.530000e-51 211.0
55 TraesCS5B01G094000 chr6A 82.609 276 42 6 269 539 56068868 56069142 3.910000e-59 239.0
56 TraesCS5B01G094000 chr6A 93.056 144 10 0 2677 2820 597219701 597219844 8.530000e-51 211.0
57 TraesCS5B01G094000 chr6A 81.159 138 17 8 121 254 108050045 108050177 5.360000e-18 102.0
58 TraesCS5B01G094000 chr6A 92.157 51 2 2 2640 2688 194459375 194459325 1.510000e-08 71.3
59 TraesCS5B01G094000 chr1B 80.456 307 49 10 277 576 32419838 32420140 1.100000e-54 224.0
60 TraesCS5B01G094000 chr1A 92.517 147 10 1 2677 2823 359901593 359901738 3.070000e-50 209.0
61 TraesCS5B01G094000 chr1A 80.603 232 33 8 2371 2594 65807737 65807964 5.210000e-38 169.0
62 TraesCS5B01G094000 chr7B 78.746 287 39 14 2372 2642 621455733 621456013 4.030000e-39 172.0
63 TraesCS5B01G094000 chr7B 87.500 56 6 1 2618 2673 695281667 695281721 2.530000e-06 63.9
64 TraesCS5B01G094000 chr3A 80.087 231 32 10 2409 2631 721673493 721673269 3.140000e-35 159.0
65 TraesCS5B01G094000 chr4B 78.652 267 35 15 2388 2642 517006847 517006591 1.130000e-34 158.0
66 TraesCS5B01G094000 chr4B 80.769 104 10 1 1620 1723 644837291 644837384 4.200000e-09 73.1
67 TraesCS5B01G094000 chr7D 77.966 177 27 10 83 254 346746892 346747061 1.930000e-17 100.0
68 TraesCS5B01G094000 chr7D 90.196 51 3 2 2639 2689 421880246 421880198 7.030000e-07 65.8
69 TraesCS5B01G094000 chr2A 92.157 51 2 2 2640 2688 474323792 474323742 1.510000e-08 71.3
70 TraesCS5B01G094000 chr2A 90.566 53 3 2 2621 2673 730128831 730128781 5.430000e-08 69.4
71 TraesCS5B01G094000 chr2A 90.385 52 3 2 2625 2676 657809346 657809297 1.950000e-07 67.6


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 TraesCS5B01G094000 chr5B 123435915 123438952 3037 True 5611.000000 5611 100.000000 1 3038 1 chr5B.!!$R2 3037
1 TraesCS5B01G094000 chr5B 123012838 123014109 1271 True 2095.000000 2095 96.337000 1377 2655 1 chr5B.!!$R1 1278
2 TraesCS5B01G094000 chr5B 123217866 123222230 4364 True 1524.666667 3498 92.738667 2 3038 3 chr5B.!!$R5 3036
3 TraesCS5B01G094000 chr5B 88340259 88341290 1031 False 1352.000000 1352 90.513000 1043 2062 1 chr5B.!!$F1 1019
4 TraesCS5B01G094000 chr5B 88210770 88212232 1462 False 603.500000 793 83.628500 759 2040 2 chr5B.!!$F2 1281
5 TraesCS5B01G094000 chr5B 123022132 123024838 2706 True 518.333333 874 90.634333 1 1381 3 chr5B.!!$R4 1380
6 TraesCS5B01G094000 chr5D 78503820 78505092 1272 False 1541.000000 1541 88.941000 892 2133 1 chr5D.!!$F4 1241
7 TraesCS5B01G094000 chr5D 78371229 78371976 747 False 774.000000 774 85.600000 1303 2040 1 chr5D.!!$F3 737
8 TraesCS5B01G094000 chr5D 78594303 78595157 854 False 554.500000 898 88.517500 860 1670 2 chr5D.!!$F7 810
9 TraesCS5B01G094000 chr5D 78361613 78362116 503 False 435.000000 435 83.301000 830 1306 1 chr5D.!!$F2 476
10 TraesCS5B01G094000 chr5A 74862989 74864174 1185 False 837.500000 1384 93.955000 894 2040 2 chr5A.!!$F2 1146


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
570 571 0.10339 TCGGTTCGTTGAGTGCTTCA 59.897 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 4425 2.579201 CGCCCTCACTGAACCGAT 59.421 61.111 0.0 0.0 0.0 4.18 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
44 45 2.231716 AACCAAGGATTAACAGGGCC 57.768 50.000 0.00 0.00 0.00 5.80
48 49 0.917333 AAGGATTAACAGGGCCGGGA 60.917 55.000 8.94 0.00 0.00 5.14
91 92 5.175126 CGATGTTAATTAAGGGTGAGTAGCG 59.825 44.000 0.00 0.00 0.00 4.26
92 93 4.186159 TGTTAATTAAGGGTGAGTAGCGC 58.814 43.478 0.00 0.00 0.00 5.92
114 115 3.809832 CCTAATTAAGCAGGGACATGTCG 59.190 47.826 19.33 7.28 0.00 4.35
148 149 4.922026 ACGCCGCGACCAAAACCT 62.922 61.111 21.79 0.00 0.00 3.50
161 162 1.128188 AAAACCTGGAGCGGAGTCCT 61.128 55.000 7.77 0.00 37.52 3.85
188 189 2.187163 GGCTCGGGCTTCACCTAC 59.813 66.667 7.48 0.00 39.10 3.18
202 203 2.171635 CCTACAAGAGGCGGTTTGC 58.828 57.895 0.00 0.00 38.96 3.68
280 281 2.105128 CGGAGGGTGCTTCTAGCG 59.895 66.667 0.00 0.00 46.26 4.26
284 285 1.935327 GAGGGTGCTTCTAGCGTCGT 61.935 60.000 0.00 0.00 46.26 4.34
290 291 1.979831 GCTTCTAGCGTCGTCGGAGT 61.980 60.000 3.90 0.00 37.56 3.85
291 292 1.284657 CTTCTAGCGTCGTCGGAGTA 58.715 55.000 3.90 0.00 37.56 2.59
312 313 0.387929 GTGTGGAGGTGTGTCTTCGA 59.612 55.000 0.00 0.00 0.00 3.71
325 326 1.676529 GTCTTCGATGGATCTCGTGGA 59.323 52.381 4.51 2.39 39.62 4.02
333 334 3.526931 TGGATCTCGTGGAATTCAGTC 57.473 47.619 7.93 0.00 0.00 3.51
373 374 2.390696 TCCGATTGGATCCGGTCTTTA 58.609 47.619 7.39 0.00 45.48 1.85
379 380 5.065988 CGATTGGATCCGGTCTTTATTTGTT 59.934 40.000 7.39 0.00 0.00 2.83
380 381 6.404293 CGATTGGATCCGGTCTTTATTTGTTT 60.404 38.462 7.39 0.00 0.00 2.83
381 382 5.637006 TGGATCCGGTCTTTATTTGTTTG 57.363 39.130 7.39 0.00 0.00 2.93
382 383 5.317808 TGGATCCGGTCTTTATTTGTTTGA 58.682 37.500 7.39 0.00 0.00 2.69
388 389 7.312154 TCCGGTCTTTATTTGTTTGATGATTG 58.688 34.615 0.00 0.00 0.00 2.67
427 428 5.639506 CCTTCTGATCTACGCTTTTCTTCAA 59.360 40.000 0.00 0.00 0.00 2.69
430 431 4.552355 TGATCTACGCTTTTCTTCAACGA 58.448 39.130 0.00 0.00 0.00 3.85
447 448 1.298041 GACGCGGTTGTTGTTGTGG 60.298 57.895 12.47 0.00 0.00 4.17
449 450 1.585002 CGCGGTTGTTGTTGTGGTG 60.585 57.895 0.00 0.00 0.00 4.17
523 524 3.912496 ATGTTTGTCTGGATCCGATGA 57.088 42.857 7.39 2.43 0.00 2.92
526 527 1.866015 TTGTCTGGATCCGATGAGGT 58.134 50.000 7.39 0.00 41.99 3.85
531 532 0.178932 TGGATCCGATGAGGTAGGGG 60.179 60.000 7.39 0.00 41.99 4.79
559 560 1.370900 CGGTTCGTCTTCGGTTCGT 60.371 57.895 0.00 0.00 37.69 3.85
561 562 0.505655 GGTTCGTCTTCGGTTCGTTG 59.494 55.000 0.00 0.00 37.69 4.10
562 563 1.480205 GTTCGTCTTCGGTTCGTTGA 58.520 50.000 0.00 0.00 37.69 3.18
563 564 1.450905 GTTCGTCTTCGGTTCGTTGAG 59.549 52.381 0.00 0.00 37.69 3.02
564 565 0.664761 TCGTCTTCGGTTCGTTGAGT 59.335 50.000 0.00 0.00 37.69 3.41
565 566 0.776451 CGTCTTCGGTTCGTTGAGTG 59.224 55.000 0.00 0.00 0.00 3.51
566 567 0.507358 GTCTTCGGTTCGTTGAGTGC 59.493 55.000 0.00 0.00 0.00 4.40
567 568 0.387929 TCTTCGGTTCGTTGAGTGCT 59.612 50.000 0.00 0.00 0.00 4.40
569 570 1.192534 CTTCGGTTCGTTGAGTGCTTC 59.807 52.381 0.00 0.00 0.00 3.86
570 571 0.103390 TCGGTTCGTTGAGTGCTTCA 59.897 50.000 0.00 0.00 0.00 3.02
576 577 3.934457 TCGTTGAGTGCTTCATAGTCA 57.066 42.857 0.00 0.00 35.27 3.41
592 593 9.775854 CTTCATAGTCATTTAGAATCTGGATGT 57.224 33.333 0.00 0.00 0.00 3.06
621 622 8.918202 TTTTTACTCCTGATGTTCATTGTACT 57.082 30.769 0.00 0.00 0.00 2.73
622 623 7.905604 TTTACTCCTGATGTTCATTGTACTG 57.094 36.000 0.00 0.00 0.00 2.74
649 650 5.962433 TGAGATCGGAAGTTTTCTCGTAAT 58.038 37.500 2.21 0.00 36.34 1.89
650 651 6.034591 TGAGATCGGAAGTTTTCTCGTAATC 58.965 40.000 2.21 0.00 36.34 1.75
698 2067 4.081087 TGAGGTAACAGAGATTTGGCCTAC 60.081 45.833 3.32 0.00 41.41 3.18
799 2168 3.475566 TCCTAGATTTGGCATCCGAAG 57.524 47.619 0.00 0.00 29.47 3.79
823 2192 4.434545 TTAGGAGGAGACGTATAGCTGT 57.565 45.455 0.00 0.00 0.00 4.40
827 2196 0.592148 GGAGACGTATAGCTGTCGGG 59.408 60.000 0.00 0.00 40.05 5.14
855 2279 3.963383 TTTGACTTGCGTCTCTTTTCC 57.037 42.857 0.00 0.00 40.86 3.13
872 2296 1.590591 TCCATCTGGAATCGGGGAAA 58.409 50.000 0.00 0.00 42.18 3.13
873 2297 1.490490 TCCATCTGGAATCGGGGAAAG 59.510 52.381 0.00 0.00 42.18 2.62
874 2298 1.312815 CATCTGGAATCGGGGAAAGC 58.687 55.000 0.00 0.00 0.00 3.51
934 2358 0.458543 CTCGACAGATCCGTGGTTGG 60.459 60.000 0.00 0.00 0.00 3.77
1026 2484 1.272769 GACTTGGACTTGTCTACGCCT 59.727 52.381 0.61 0.00 0.00 5.52
1188 2685 0.299300 CGTTCGTGTCGAGCAACAAA 59.701 50.000 6.78 0.00 36.94 2.83
1199 2696 2.030893 CGAGCAACAAAGCATTCTTGGA 60.031 45.455 0.00 0.00 36.85 3.53
1281 2952 2.844348 GACCCATCTCCTGAACCCTAAA 59.156 50.000 0.00 0.00 0.00 1.85
1314 2985 1.244816 TCGAGCTTCCGACTCTCAAA 58.755 50.000 0.00 0.00 33.14 2.69
1329 3000 0.824595 TCAAAGACGACGAGGTCCCA 60.825 55.000 0.00 0.00 37.66 4.37
2725 4444 4.003788 CGGTTCAGTGAGGGCGGT 62.004 66.667 0.00 0.00 0.00 5.68
2899 4618 1.482177 CGGATCCTCCCTCATTCTCCT 60.482 57.143 10.75 0.00 31.13 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.037605 GTCACTTACAGTGGGTCCCG 60.038 60.000 2.65 0.00 45.94 5.14
48 49 1.887198 CGAGAGTCACTTACAGTGGGT 59.113 52.381 4.09 0.00 45.94 4.51
57 58 7.042335 CCCTTAATTAACATCGAGAGTCACTT 58.958 38.462 0.00 0.00 0.00 3.16
67 68 5.175126 CGCTACTCACCCTTAATTAACATCG 59.825 44.000 0.00 0.00 0.00 3.84
91 92 3.555966 ACATGTCCCTGCTTAATTAGGC 58.444 45.455 12.39 12.39 32.58 3.93
92 93 3.809832 CGACATGTCCCTGCTTAATTAGG 59.190 47.826 20.03 0.00 0.00 2.69
114 115 4.966787 TGCAAACCCCGGCAGACC 62.967 66.667 0.00 0.00 34.58 3.85
188 189 2.629656 CCCTGCAAACCGCCTCTTG 61.630 63.158 0.00 0.00 41.33 3.02
209 210 3.636231 CTCCAACGGGACCAGCCA 61.636 66.667 0.00 0.00 38.64 4.75
213 214 3.636231 CCAGCTCCAACGGGACCA 61.636 66.667 0.00 0.00 38.64 4.02
280 281 1.154338 CCACACGTACTCCGACGAC 60.154 63.158 2.55 0.00 45.82 4.34
284 285 1.073722 ACCTCCACACGTACTCCGA 59.926 57.895 0.00 0.00 40.70 4.55
290 291 1.338973 GAAGACACACCTCCACACGTA 59.661 52.381 0.00 0.00 0.00 3.57
291 292 0.104304 GAAGACACACCTCCACACGT 59.896 55.000 0.00 0.00 0.00 4.49
312 313 3.452264 TGACTGAATTCCACGAGATCCAT 59.548 43.478 2.27 0.00 0.00 3.41
325 326 4.273480 CCGAAGACAAACACTGACTGAATT 59.727 41.667 0.00 0.00 30.01 2.17
333 334 1.948104 TCCACCGAAGACAAACACTG 58.052 50.000 0.00 0.00 0.00 3.66
357 358 6.435904 TCAAACAAATAAAGACCGGATCCAAT 59.564 34.615 9.46 0.00 0.00 3.16
373 374 7.288810 ACCTACACACAATCATCAAACAAAT 57.711 32.000 0.00 0.00 0.00 2.32
379 380 4.979335 TCCAACCTACACACAATCATCAA 58.021 39.130 0.00 0.00 0.00 2.57
380 381 4.632327 TCCAACCTACACACAATCATCA 57.368 40.909 0.00 0.00 0.00 3.07
381 382 4.576463 GGATCCAACCTACACACAATCATC 59.424 45.833 6.95 0.00 0.00 2.92
382 383 4.228210 AGGATCCAACCTACACACAATCAT 59.772 41.667 15.82 0.00 38.65 2.45
388 389 3.260884 TCAGAAGGATCCAACCTACACAC 59.739 47.826 15.82 0.00 39.62 3.82
427 428 2.101835 ACAACAACAACCGCGTCGT 61.102 52.632 4.92 0.00 0.00 4.34
430 431 2.041686 ACCACAACAACAACCGCGT 61.042 52.632 4.92 0.00 0.00 6.01
447 448 1.224592 CCCCATAGGACCAGCACAC 59.775 63.158 0.00 0.00 38.24 3.82
449 450 0.331616 AAACCCCATAGGACCAGCAC 59.668 55.000 0.00 0.00 39.89 4.40
523 524 2.838225 CCGTCATCGCCCCTACCT 60.838 66.667 0.00 0.00 35.54 3.08
544 545 1.066002 ACTCAACGAACCGAAGACGAA 59.934 47.619 0.00 0.00 42.66 3.85
546 547 0.776451 CACTCAACGAACCGAAGACG 59.224 55.000 0.00 0.00 39.43 4.18
548 549 0.387929 AGCACTCAACGAACCGAAGA 59.612 50.000 0.00 0.00 0.00 2.87
553 554 3.326747 ACTATGAAGCACTCAACGAACC 58.673 45.455 0.00 0.00 37.67 3.62
559 560 9.102757 GATTCTAAATGACTATGAAGCACTCAA 57.897 33.333 0.00 0.00 37.67 3.02
561 562 8.763356 CAGATTCTAAATGACTATGAAGCACTC 58.237 37.037 0.00 0.00 0.00 3.51
562 563 7.714377 CCAGATTCTAAATGACTATGAAGCACT 59.286 37.037 0.00 0.00 0.00 4.40
563 564 7.712639 TCCAGATTCTAAATGACTATGAAGCAC 59.287 37.037 0.00 0.00 0.00 4.40
564 565 7.795047 TCCAGATTCTAAATGACTATGAAGCA 58.205 34.615 0.00 0.00 0.00 3.91
565 566 8.719648 CATCCAGATTCTAAATGACTATGAAGC 58.280 37.037 2.68 0.00 0.00 3.86
566 567 9.775854 ACATCCAGATTCTAAATGACTATGAAG 57.224 33.333 12.15 0.00 0.00 3.02
603 604 3.264193 AGGCAGTACAATGAACATCAGGA 59.736 43.478 0.00 0.00 0.00 3.86
620 621 2.393271 AACTTCCGATCTCAAGGCAG 57.607 50.000 5.72 0.00 0.00 4.85
621 622 2.859165 AAACTTCCGATCTCAAGGCA 57.141 45.000 5.72 0.00 0.00 4.75
622 623 3.339141 AGAAAACTTCCGATCTCAAGGC 58.661 45.455 5.72 0.00 0.00 4.35
649 650 4.862371 GGGTTTAGTCCCCATTGTAATGA 58.138 43.478 6.18 0.00 42.15 2.57
728 2097 3.329814 ACGGGACTCCCTAAAATCTGTTT 59.670 43.478 12.62 0.00 42.67 2.83
729 2098 2.910977 ACGGGACTCCCTAAAATCTGTT 59.089 45.455 12.62 0.00 42.67 3.16
730 2099 2.236395 CACGGGACTCCCTAAAATCTGT 59.764 50.000 12.62 0.00 42.67 3.41
735 2104 1.203212 TCCTCACGGGACTCCCTAAAA 60.203 52.381 12.62 0.00 42.67 1.52
736 2105 0.410663 TCCTCACGGGACTCCCTAAA 59.589 55.000 12.62 0.00 42.67 1.85
799 2168 5.474189 ACAGCTATACGTCTCCTCCTAATTC 59.526 44.000 0.00 0.00 0.00 2.17
827 2196 1.281656 CGCAAGTCAAAACCGGACC 59.718 57.895 9.46 0.00 35.89 4.46
855 2279 1.312815 GCTTTCCCCGATTCCAGATG 58.687 55.000 0.00 0.00 0.00 2.90
872 2296 5.656900 ATATATATATAGGGGGCTGGGCT 57.343 43.478 3.27 0.00 0.00 5.19
873 2297 5.363005 CGTATATATATATAGGGGGCTGGGC 59.637 48.000 18.63 3.42 31.10 5.36
874 2298 6.500336 ACGTATATATATATAGGGGGCTGGG 58.500 44.000 25.41 7.94 36.14 4.45
934 2358 2.359230 AAGCGGCACAAGGCTCTC 60.359 61.111 1.45 0.00 44.01 3.20
1026 2484 2.743664 CAAATCCATCGCTGACAACAGA 59.256 45.455 0.00 0.00 46.03 3.41
1188 2685 1.448540 CGGCGTCTCCAAGAATGCT 60.449 57.895 0.00 0.00 31.04 3.79
1281 2952 2.028130 AGCTCGATTCTTGATCCGTCT 58.972 47.619 0.00 0.00 0.00 4.18
1314 2985 2.052690 CCATGGGACCTCGTCGTCT 61.053 63.158 2.85 0.00 32.65 4.18
1329 3000 4.314440 ACGCACCTGCACGTCCAT 62.314 61.111 0.00 0.00 38.28 3.41
2706 4425 2.579201 CGCCCTCACTGAACCGAT 59.421 61.111 0.00 0.00 0.00 4.18
2725 4444 0.871722 CCATTTGGTGACTTTCGCGA 59.128 50.000 3.71 3.71 0.00 5.87
2834 4553 1.195115 CAACCGGGATCTCCTTGAGA 58.805 55.000 6.32 0.00 43.20 3.27
2899 4618 3.808466 AGCGTCTTATCAAGATCTGCA 57.192 42.857 0.00 0.00 40.18 4.41



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

AutoCloner maintained by Alex Coulton.